How to annotate a gene with the cytogenetic band

how to
Author

Haky Im

Published

July 28, 2021

Adding the cytogenetic to genes is convenient because it provides a somewhat memorable names for the genomic region where the gene is located. Biomart package in bioconductor has the database and function for the annnotation.

Code
suppressMessages(library(tidyverse))
suppressMessages(library(glue))
suppressMessages(library(RSQLite))

add cytogenetic band to genes

Code
# install biomaRt if not installed 
# if (!requireNamespace("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# BiocManager::install("biomaRt")
## YOU MAY WANT TO RESTART R/RSTUDIO AFTER INSTAALLING BIOCMANAGER
library(biomaRt)

#ensembl <- useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl")


ensembl <- useEnsembl(biomart = "ensembl", 
                   dataset = "hsapiens_gene_ensembl", 
                   mirror = "useast")
Note

mirror = “useast” was necessary to make quarto render work; interactive runs seems to be able to be redirected to the useast mirror automatically but not quarto render

Code
## get the gene annotation with cytoband  from biomart
anno_gene <- getBM(attributes =c("ensembl_gene_id","external_gene_name","chromosome_name","start_position","end_position","band", "gene_biotype"),mart=ensembl)

## define function to add cytoband to gene
addband2gene = function(df,geneid = "ensembl_gene_id")
{
  if(!exists("anno_gene"))
  {
    ensembl <- useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl")
    anno_gene <<- getBM(attributes = c("ensembl_gene_id","external_gene_name","chromosome_name","start_position","end_position","band", "gene_biotype"),mart=ensembl )
  print("defined anno_gene")
  }
  if(geneid != "ensembl_gene_id") names(df)[names(df)==geneid] = "ensembl_gene_id" ## this is an ugly workaround - need to find a way to use rename_ for this but don't know how to specify a string instead of name in rename(geneid = "ensembl_gene_id")
  df = df %>% left_join(anno_gene, by=c( "ensembl_gene_id" ))
  if(geneid != "ensembl_gene_id") names(df)[names(df)=="ensembl_gene_id"] = geneid
  df %>% mutate(cytoband = paste0(chromosome_name,band))
}
anno_gene <- anno_gene %>% mutate(cytoband = paste0(chromosome_name,band))

To get start and end of the cytegenetic bands

Code
## Download cytoband table from http://genome.ucsc.edu/cgi-bin/hgTables
## 1. Go to the UCSC Genome browser: https://genome.ucsc.edu/index.html
## 2. Mouse over "Tools" and select "Table Browser"
## 3. In the table browser window, set the following parameters: clade = mammal, genome = human, assembly = hg38 (or other), group = Mapping and Sequencing, track = Chromosome Band, table = cytoBand, position = chr1 (or whatever chromosome you are interested in), output format = all fields from selected table, file type returned = plain text
## 4. Click [get output]
## The results will show the following 5 columns: chromosome number, cytoband start position, end position, cytoband name, and staining result.
## Haynes, Karmella. (2018). Re: How can i gen the length in mb from a cytoband?. Retrieved from: https://www.researchgate.net/post/How-can-i-gen-the-length-in-mb-from-a-cytoband/5b2147a0565fba5e2820b3de/citation/download.
#

WEBDATA="/Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data"
cytoband_hg38 <- read_table(glue("{WEBDATA}/2021-07-28-how-to-get-the-cytogenetic-band-of-a-gene/hgTables-cytoband-positions-hg38.txt"),comment = "#",guess_max = 10000)

── Column specification ────────────────────────────────────────────────────────
cols(
  chrom = col_character(),
  chromStart = col_double(),
  chromEnd = col_double(),
  name = col_character(),
  gieStain = col_character()
)
Warning: 571 parsing failures.
row col  expected    actual                                                                                                                                                                                  file
455  -- 5 columns 4 columns '/Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data/2021-07-28-how-to-get-the-cytogenetic-band-of-a-gene/hgTables-cytoband-positions-hg38.txt'
864  -- 5 columns 4 columns '/Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data/2021-07-28-how-to-get-the-cytogenetic-band-of-a-gene/hgTables-cytoband-positions-hg38.txt'
865  -- 5 columns 4 columns '/Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data/2021-07-28-how-to-get-the-cytogenetic-band-of-a-gene/hgTables-cytoband-positions-hg38.txt'
866  -- 5 columns 4 columns '/Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data/2021-07-28-how-to-get-the-cytogenetic-band-of-a-gene/hgTables-cytoband-positions-hg38.txt'
867  -- 5 columns 4 columns '/Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data/2021-07-28-how-to-get-the-cytogenetic-band-of-a-gene/hgTables-cytoband-positions-hg38.txt'
... ... ......... ......... .....................................................................................................................................................................................
See problems(...) for more details.
Code
#
cytoband_hg37 <- read_table(glue("{WEBDATA}/2021-07-28-how-to-get-the-cytogenetic-band-of-a-gene/hgTables-cytoband-positions-hg37.txt"),comment = "#",guess_max = 10000)

── Column specification ────────────────────────────────────────────────────────
cols(
  chrom = col_character(),
  chromStart = col_double(),
  chromEnd = col_double(),
  name = col_character(),
  gieStain = col_character()
)
Code
# What's the distribution of the weights

cytoband_hg38 %>% filter(chrom %in% paste0("chr",c(1:22)) )%>%  mutate(bandw = chromEnd - chromStart) %>% .[["bandw"]] %>% summary()/1e6
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.100   2.000   3.200   3.545   4.600  18.100 
Code
  #  Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  # 0.100   2.000   3.200   3.545   4.600  18.100 
cytoband_hg37 %>% filter(chrom %in% paste0("chr",1:2) ) %>%  mutate(bandw = chromEnd - chromStart) %>% .[["bandw"]] %>% summary()/1e6
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   0.50    2.40    3.60    3.94    4.90   15.20 
Code
  #  Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  # 0.100   2.100   3.300   3.552   4.600  15.200 

cytoband_hg37 %>% mutate(bandw = chromEnd - chromStart) %>% ggplot(aes(bandw,fill=chrom)) + geom_density(alpha=0.5)

Code
# How many cytogenetic bands are there in the autosomes (non sex chromosomes nor mitochondria)

dim(cytoband_hg38)
[1] 1433    5
Code
dim(cytoband_hg37)
[1] 862   5
Code
## there are many more cytobands in hg38 because there are many patches added after the official release of hg19
Code
## number of genes per cytoband
anno_gene %>% count(cytoband) %>% arrange(desc(n))
                                   cytoband   n
1                                   16p11.2 457
2                                   14q11.2 434
3                                   16p13.3 432
4                                   19p13.3 389
5                                   11p15.4 386
6                                   17p11.2 369
7                   CHR_HSCHR6_MHC_COX_CTG1 340
8                                   19p13.2 326
9                   CHR_HSCHR6_MHC_QBL_CTG1 322
10                  CHR_HSCHR6_MHC_DBB_CTG1 316
11                                  17q11.2 311
12                 CHR_HSCHR6_MHC_SSTO_CTG1 303
13                 CHR_HSCHR6_MHC_MANN_CTG1 299
14                                 14q32.33 292
15                  CHR_HSCHR6_MHC_MCF_CTG1 292
16                                   8p23.1 284
17                                  15q11.2 274
18                                  19q13.2 271
19                                 19q13.42 268
20                                  17q25.3 267
21                                   1q21.3 267
22                                    17q12 262
23                                  3p21.31 262
24                                   2p11.2 260
25                                   1q32.1 252
26                                     Xq28 249
27                                  11q12.1 247
28                                 12p13.31 247
29                                   6p22.1 247
30                                 22q11.21 245
31                                   7q22.1 237
32                                 19q13.33 231
33                                  17p13.1 228
34                                   8q24.3 227
35                                  16q22.1 223
36                                  21q22.3 218
37                                     7q34 217
38                                 19p13.11 216
39                                  7q11.21 213
40                                 17q21.31 208
41                           CHR_HG76_PATCH 207
42                                 12q24.31 199
43                                     3q29 198
44                                    19p12 197
45                                 12q13.13 196
46                                  7q11.23 196
47                                 19q13.43 193
48                                  11q13.4 191
49                                  11q13.1 190
50                                  17q21.2 188
51                                   5q31.3 188
52                                     6q21 188
53                       CHR_HSCHR14_3_CTG1 188
54                                  11q23.3 187
55                                   5q35.3 187
56                                     1q44 186
57                                   9q34.3 184
58                                   1p31.1 183
59                  CHR_HSCHR6_MHC_APD_CTG1 183
60                                     2q35 181
61                                  14q24.3 179
62                                  17q25.1 177
63                                   6p21.1 174
64                                  15q26.1 172
65                                   1p32.3 172
66                                  6p21.33 171
67                                 19q13.12 168
68                                   5q31.1 168
69                                 20q13.33 167
70                                   9p13.3 167
71                                   2q31.1 165
72                                   Yp11.2 165
73                                  11p11.2 162
74                                    14q12 162
75                                 19q13.41 162
76                                  1p36.33 162
77                                   7p11.2 162
78                                  11p15.5 161
79                                 12q24.33 161
80                                    20p13 161
81                                  1p36.11 159
82                                 20q13.12 159
83                                   7q36.1 156
84                                 18p11.21 155
85                                   2q37.3 155
86                                 19q13.32 154
87                                   4p16.3 153
88                                   1q21.1 151
89                                 22q11.22 151
90                                   2q37.1 150
91                                   4p16.1 149
92                                   6p22.3 148
93                                     6q27 148
94                                   1p34.2 147
95                                   2q11.2 146
96                                   1p31.3 145
97                                   2q33.1 145
98                                    17q22 144
99                                   1p34.3 144
100                                 Xp11.23 143
101                                 22q12.3 142
102                                 22q13.1 142
103                                  2q21.1 142
104                                 11q13.2 141
105                                  1q21.2 141
106                                 17p13.3 139
107                                  1q23.3 139
108                                14q32.31 138
109                                  5q11.2 138
110                                19p13.12 137
111                                   16q21 136
112                                 9q34.11 135
113                                    1q41 133
114                                 1p36.13 132
115                                21q22.11 132
116                                 11q24.2 131
117                                 16q12.1 131
118                                    4q12 131
119                                  1p13.3 130
120                                  2p23.3 130
121                                 1q42.13 129
122                                17q21.32 128
123                                22q11.23 127
124                                 Xp11.22 127
125                                 16q23.1 126
126                                 15q15.1 125
127                                 17p13.2 125
128                                    2p21 125
129                                 18q11.2 124
130                                 22q12.2 123
131                                 22q13.2 123
132                                 15q26.3 122
133                                 8q21.13 122
134                                 15q21.1 121
135                                   13q34 120
136                                 11p15.1 119
137                                 14q32.2 119
138                                 16p12.3 119
139                                  1q25.3 119
140                                    8p12 119
141                                  Xq13.1 119
142                                 15q25.2 118
143                                  2p25.1 118
144                                  Xp22.2 118
145                                  3q21.3 117
146                                  Xq26.3 117
147                                   12q12 116
148                                 1p36.12 116
149                                  5q13.2 116
150                                  Xq22.1 116
151                                 11q14.1 115
152                                 1p36.22 115
153                                12q13.12 114
154                                    4q25 114
155                                  7p14.3 114
156                                 18q21.1 113
157                                    1q43 113
158                       CHR_HSCHR7_2_CTG6 113
159                                 10q26.3 112
160                                  1p13.2 112
161                                    Xq24 112
162                                Yq11.223 112
163                                 10q22.1 111
164                                   15q14 111
165                                 15q25.1 111
166                                   17p12 111
167                                  5q14.3 111
168                                    5q32 111
169                                  8q22.3 111
170                                    Xq23 111
171                                 Yq11.23 111
172                                 11q22.3 110
173                                15q22.31 110
174                                  4q13.3 108
175                                   11p13 107
176                                 15q21.3 107
177                                  8q22.1 107
178                                10q11.21 106
179                                   15q23 106
180                                17q21.33 106
181                                19q13.11 106
182                                 6p21.32 106
183                      CHR_HSCHR17_7_CTG4 106
184                                13q12.11 105
185                                   18q23 105
186                                  7p14.1 105
187                                20q11.21 104
188                                  2q14.1 104
189                                  6p22.2 104
190                                  1p34.1 103
191                                13q14.11 102
192                                 1p36.21 102
193                                 5p15.33 102
194                                  8p21.3 102
195                                 12q23.3 101
196                                 15q22.2 101
197                                20q11.23 101
198                                  6q25.3 101
199                                 11q12.3 100
200                                   11q21 100
201                                 16p12.2 100
202                                  6q14.1 100
203                                 10q22.2  99
204                                20p11.21  99
205                                  3p22.1  99
206                                    4p14  99
207                                 10p12.1  98
208                                 22q11.1  98
209                                    5q15  98
210                                  1q23.1  97
211                                22q13.31  97
212                                  4q32.1  97
213                                  7p22.1  97
214                                    9q13  97
215                                10q11.22  96
216                                 12p13.2  96
217                                 12q13.2  96
218                                 16q24.1  96
219                                    2q13  96
220                                  4q35.1  96
221                                 11q14.3  95
222                                12q13.11  95
223                                 12q23.1  95
224                                 21p11.2  95
225                                 21q21.1  95
226                                 6p21.31  95
227                                Yq11.222  95
228                                  2q14.3  94
229                                  7q21.3  94
230                                 8q24.13  94
231                                19q13.31  93
232                                20q11.22  93
233                                   10p13  92
234                                20q13.13  92
235                                    2p14  92
236                                 10q22.3  91
237                                  3p25.3  91
238                                  3q22.1  91
239                                  4q13.2  91
240                                  5q14.1  91
241                                  5q35.2  91
242                                 18q12.1  90
243                                    1q22  90
244                                 22q12.1  90
245                                  5q23.2  90
246                                  6q25.1  90
247                                    2p12  89
248                                    8p22  89
249                                 9q21.11  89
250                                  Xp11.3  89
251                                  Xp11.4  89
252                                  2q33.3  88
253                                    6q13  88
254                                  9p21.3  88
255                                12p13.33  87
256                                 12q13.3  87
257                                 15q21.2  87
258                                    3q23  87
259                                  5q35.1  87
260                                  6q23.2  87
261                                  2p13.3  86
262                                  3q25.1  86
263                                    7q33  86
264                                  9p24.1  86
265                                   12q15  85
266                                 13q14.3  85
267                                 16p12.1  85
268                                18p11.31  85
269                                  1p35.3  85
270                                  1q24.2  85
271                                22q13.33  85
272                                  5p13.2  85
273                                  5q31.2  85
274                                  5q33.3  85
275                                  8q12.1  85
276                                 15q24.1  84
277                                16p13.11  84
278                                    1p33  84
279                                  1q42.2  84
280                                  2p16.1  84
281                                  7p15.2  84
282                                  9q33.3  84
283                                12p11.21  83
284                                 12p12.1  83
285                                 17q24.2  83
286                                  4q22.1  83
287                                  4q31.3  83
288                                    7q35  83
289                                10q26.13  82
290                                   12q22  82
291                                    4q24  82
292                                   10p14  81
293                                  2q11.1  81
294                                  4q35.2  80
295                                  5q13.3  80
296                                    6q15  80
297                                  7p22.3  80
298                                 9q22.33  80
299                                  9q31.1  80
300                                 17q23.2  79
301                                  1q32.2  79
302                                 3q26.33  79
303                                    4q26  79
304                      CHR_HSCHR15_4_CTG8  79
305                                 10q21.3  78
306                                12q24.11  78
307                                 14q22.1  78
308                                 14q23.1  78
309                                 16q24.3  78
310                                  3p22.2  78
311                                 5p15.31  78
312                                  7p15.3  78
313                                  7q32.1  78
314                                 8p11.21  78
315                                  Xq21.1  78
316                                 10p15.1  77
317                                 13q14.2  77
318                                 16q12.2  77
319                                  1q25.2  77
320                                  3p25.1  77
321                                10q23.31  76
322                                20p11.23  76
323                                  2p25.3  76
324                                 11q12.2  75
325                                 12p12.3  75
326                                  4q28.3  75
327                                  5p13.3  75
328                                  6p21.2  75
329                    CHR_HSCHR19_4_CTG3_1  75
330                                 11q23.1  74
331                                 12q14.1  74
332                                  1p22.1  74
333                                  1p35.2  74
334                                  2p13.1  74
335                                 4q31.21  74
336                                  6p12.3  74
337                                 6q22.31  74
338                                  9p11.2  74
339                                 14q24.2  73
340                                16p13.13  73
341                                 21q21.3  73
342                                 3q13.33  73
343                                  4p15.2  73
344                                  5p15.1  73
345                                  5p15.2  73
346                                  7q36.3  73
347                                  8q21.3  73
348                                 9q22.31  73
349                                 9q22.32  73
350                                 1p36.32  72
351                                  1q32.3  72
352                                    2p15  72
353                                  4q32.3  72
354                                  5q23.1  72
355                                    7p13  72
356                                    9q32  72
357                                  Xq27.3  71
358                                 15q24.2  70
359                                 15q26.2  70
360                                  3q27.1  70
361                                  4q21.1  70
362                                    5q34  70
363                                  7q31.1  70
364                                19p13.13  69
365                                   19q12  69
366                                  9q33.2  69
367                                 10q25.3  68
368                                 12q21.2  68
369                                12q24.32  68
370                                  1q23.2  68
371                                  2p24.1  68
372                                  3p14.1  68
373                                    3q24  68
374                                  6p12.1  68
375                                  6q23.3  68
376                                  7p21.3  68
377                                 8q24.22  68
378                                 14q24.1  67
379                                 17q23.3  67
380                                 18q21.2  67
381                                  1p22.2  67
382                                 20p12.1  67
383                                  3q26.2  67
384                                 7q21.11  67
385                                10q24.32  66
386                                 14q23.3  66
387                                18p11.32  66
388                                  3p14.3  66
389                                  8p21.2  66
390                                10p11.21  65
391                                18p11.22  65
392                                    1p12  65
393                                 21q11.2  65
394                                  3p24.3  65
395                                  7p21.1  65
396                                    Xq25  65
397                                10q23.33  64
398                                 11q24.1  64
399                                 13q31.1  64
400                                 14q21.3  64
401                                   16q13  64
402                                    3p13  64
403                                10q11.23  63
404                                11p11.12  63
405                                13q12.12  63
406                                  1p21.3  63
407                                  2q36.3  63
408                                  3p21.1  63
409                                  3q27.3  63
410                                  5p13.1  63
411                                  6p25.2  63
412                                 9q21.13  63
413                                 15q13.1  62
414                                 15q13.2  62
415                                  1p22.3  62
416                                  1q42.3  62
417                                  2q24.2  62
418                                  3q11.2  62
419                                  Xq13.2  62
420                                10p12.31  61
421                                 11q14.2  61
422                                 13q12.3  61
423                                 15q25.3  61
424                                 20p12.3  61
425                                  2q32.1  61
426                                    2q34  61
427                                  3p22.3  61
428                                12q21.31  60
429                                 13q13.3  60
430                                14q32.12  60
431                                 16q22.2  60
432                                 20q13.2  60
433                                  2q24.1  60
434                        CHR_HG2365_PATCH  60
435                                 Xp11.21  60
436                                 Xp22.33  60
437                                  1q25.1  59
438                                 21q22.2  59
439                                  2p22.3  59
440                                  3p21.2  59
441                                    5p12  59
442                                 8q24.21  59
443                           CHR_HG1_PATCH  59
444                      CHR_HSCHR16_1_CTG1  59
445                                 10q23.1  58
446                                12q24.23  58
447                                 15q13.3  58
448                                 16q24.2  58
449                                  1p21.2  58
450                                  3p12.3  58
451                                  5q33.1  58
452                                  7q22.3  58
453                                  7q31.2  58
454                                 8p11.23  58
455                                  8q22.2  58
456                                 10q21.1  57
457                                   11q25  57
458                                 14q22.3  57
459                                 16p11.1  57
460                                  3q21.2  57
461                                 11q24.3  56
462                                12p13.32  56
463                                 14q21.1  56
464                                 18q12.2  56
465                                 1q42.12  56
466                                  2p16.3  56
467                                  2q12.1  56
468                                  2q31.2  56
469                                 8q21.11  56
470                                 11q13.3  55
471                                12q21.33  55
472                                 13q32.3  55
473                                18q21.32  55
474                                  3q26.1  55
475                                  5q21.1  55
476                                 8q11.23  55
477                                  9q31.3  55
478                                  Xp21.1  55
479                                  Xq22.3  55
480                                  Xq26.2  55
481                                  1p35.1  54
482                                 3q26.31  54
483                                  4q13.1  54
484                                  4q34.1  54
485                                  6q22.1  54
486                                  8p23.3  54
487                                  9p21.1  54
488                                 11q13.5  53
489                                 12q14.2  53
490                                  2q32.3  53
491                                 3q13.31  53
492                                  6p24.3  53
493                                 8q11.21  53
494                     CHR_HSCHR5_2_CTG1_1  53
495                                10p11.22  52
496                                 10q23.2  52
497                                 12q14.3  52
498                                 16q23.2  52
499                                 18q12.3  52
500                                 18q22.3  52
501                                 1p36.23  52
502                                20q13.32  52
503                                  6p25.1  52
504                                  7p12.3  52
505                                  7p14.2  52
506                                 9q21.33  52
507              CHR_HSCHR19LRC_PGF1_CTG3_1  52
508                                 10q24.1  51
509                                 10q25.2  51
510                                12q24.13  51
511                                13q12.13  51
512                                  2q21.2  51
513                                  2q23.3  51
514                                  3q13.2  51
515                                  3q22.3  51
516                                10q26.11  50
517                                 12p13.1  50
518                                 14q31.3  50
519                                 18q22.1  50
520                                  5q12.1  50
521                                  6q14.3  50
522                                  6q16.1  50
523                                  8q12.3  50
524                                 9q21.32  50
525                                 9q34.13  50
526                                 11p14.1  49
527                                 12q23.2  49
528                                14q32.13  49
529                                  2q24.3  49
530                                 3q25.31  49
531                                  4p15.1  49
532                                  4q28.1  49
533                                    6q12  49
534                                  6q25.2  49
535                                12p11.22  48
536                                 12q21.1  48
537                                 13q31.3  48
538                                 13q32.1  48
539                                  1q24.3  48
540                                  2q32.2  48
541                                    4p13  48
542                                    4q23  48
543                                  4q31.1  48
544                                 10q25.1  47
545                                   11q11  47
546                                 11q23.2  47
547                                 15q15.3  47
548                                  1q24.1  47
549                                  2p24.3  47
550                                  2q14.2  47
551                                  2q36.1  47
552                                 3q13.13  47
553                                  6q24.1  47
554              CHR_HSCHR19LRC_COX1_CTG3_1  47
555                                10p11.23  46
556                                 10q24.2  46
557                                 16p13.2  46
558                                  1q31.1  46
559                                  2p22.1  46
560                                  2q22.1  46
561                                  5q12.3  46
562                                  6q24.2  46
563                                  8p21.1  46
564                                  9q34.2  46
565                                  Xp21.3  46
566                                   11p12  45
567                                 14q23.2  45
568                                 17q24.3  45
569                                18q21.33  45
570                                21q22.13  45
571                                  2q22.3  45
572                                  9q31.2  45
573                                 10p15.3  44
574                                10q24.31  44
575                                12q24.21  44
576                                13q14.13  44
577                                14q32.11  44
578                                  1p13.1  44
579                                 20p12.2  44
580                                  2p22.2  44
581                                  8q23.1  44
582                      CHR_HSCHR17_2_CTG5  44
583                                 11p15.3  43
584                                 1p36.31  43
585                                  1q31.3  43
586                                21q22.12  43
587                                  3p24.1  43
588                                 4p15.32  43
589                                 7q31.32  43
590                                  7q32.2  43
591                                 Xp22.11  43
592                                 14q31.1  42
593                                 16q23.3  42
594                                20q13.31  42
595                                  3q25.2  42
596                                  4q34.3  42
597                                  9p13.2  42
598                                 15q24.3  41
599                                 17q24.1  41
600                                   20q12  41
601                                  2q33.2  41
602                                 3q26.32  41
603                                    3q28  41
604                                    4p12  41
605                                    4q27  41
606                                  5p14.1  41
607                                  6q24.3  41
608                                  8q13.1  41
609                                  8q13.3  41
610                                  9q22.1  41
611                        CHR_HG2290_PATCH  41
612                                 Xp22.31  41
613                                 14q13.2  40
614                                 14q21.2  40
615                                  1p11.2  40
616                                 6q22.33  40
617                                  8q21.2  40
618                      CHR_HSCHR17_1_CTG5  40
619                                 Xq21.31  40
620                                 10q26.2  39
621                                   21p12  39
622                                 4p15.33  39
623                                  5q21.3  39
624                                  6p25.3  39
625                      CHR_HSCHR15_6_CTG8  39
626                                  Xq22.2  39
627                                13q21.33  38
628                                18q21.31  38
629                                  1q31.2  38
630                                  3p14.2  38
631                                 4q21.21  38
632                                 4q21.22  38
633                                  5q33.2  38
634                                  7p12.1  38
635                                 8q24.12  38
636                                    9p23  38
637                                  9p24.3  38
638                                 13q22.3  37
639                                16p13.12  37
640                                  2p23.2  37
641                                  2q12.3  37
642                                  3p25.2  37
643                                  5p14.3  37
644                                    6q26  37
645                                  9q33.1  37
646                      CHR_HSCHR14_7_CTG1  37
647              CHR_HSCHR19LRC_PGF2_CTG3_1  37
648                                      MT  37
649                                 11p14.3  36
650                                 11p15.2  36
651                                 13q33.3  36
652                                  9p22.3  36
653                                  Xq26.1  36
654                                Yq11.221  36
655                                 13q33.1  35
656                                 17q23.1  35
657                                  3p26.1  35
658                                  3q21.1  35
659                                  6p12.2  35
660                                  7q21.2  35
661                                    Xq12  35
662                                 Xq21.33  35
663                                   15q12  34
664                                  1p21.1  34
665                                 21q21.2  34
666                                  3p24.2  34
667                                 7q21.13  34
668                         CHR_HG109_PATCH  34
669                      CHR_HSCHR22_1_CTG7  34
670                                 10q21.2  33
671                                 13q12.2  33
672                                 7q11.22  33
673                                 7q31.33  33
674                                  9q22.2  33
675                                    4p11  32
676                                 4q21.23  32
677                                 4q31.23  32
678                                  5q22.3  32
679                                  8p23.2  32
680                 CHR_HG1342_HG2282_PATCH  32
681                                 10p12.2  31
682                                10q24.33  31
683                                 11q22.1  31
684                                   13q11  31
685                                 13q13.1  31
686                                14q32.32  31
687                                  1p32.1  31
688                                  2q12.2  31
689                                  2q31.3  31
690                                  3q12.3  31
691                                 3q13.12  31
692                                  7q32.3  31
693                                  9p21.2  31
694                      CHR_HSCHR12_3_CTG2  31
695              CHR_HSCHR19LRC_COX2_CTG3_1  31
696                                 Yq11.21  31
697                                 10p11.1  30
698                                12p11.23  30
699                                 13q21.1  30
700                                 3q25.32  30
701                                  6q16.3  30
702                                  8q11.1  30
703                      CHR_HSCHR17_3_CTG1  30
704                                  Xq27.1  30
705                                 11q22.2  29
706                                 15q15.2  29
707                                  2p16.2  29
708                                  5q22.1  29
709                                    6p23  29
710                                  6p24.2  29
711                          CHR_HG30_PATCH  29
712                                 Xp22.12  29
713                                13q21.31  28
714                                 14q13.3  28
715                                  2p23.1  28
716                                 3q25.33  28
717                                    4q33  28
718                                  5q23.3  28
719                                 7q21.12  28
720                                  9p11.1  28
721                                  1p32.2  27
722                                 20q11.1  27
723                                 5p15.32  27
724                                 7q31.31  27
725                                  8q23.3  27
726                                    9p12  27
727                                  9p13.1  27
728                                  9p24.2  27
729                                12q24.22  26
730                                  2p25.2  26
731                                  2q21.3  26
732                                  3p26.3  26
733                                  3q12.1  26
734                                  5q13.1  26
735                                  8q13.2  26
736                                  9p22.1  26
737                                  9q21.2  26
738                          CHR_HG26_PATCH  26
739                      CHR_HSCHR12_2_CTG2  26
740                      CHR_HSCHR17_4_CTG4  26
741                                 Xp22.13  26
742                                10q23.32  25
743                                 13q31.2  25
744                                 15q11.1  25
745                                  2p13.2  25
746                                  2p24.2  25
747                                  4q28.2  25
748                                  7q36.2  25
749                                 8p11.22  25
750                                 9q21.12  25
751                        CHR_HG1815_PATCH  25
752                        CHR_HG2023_PATCH  25
753                      CHR_HSCHR15_1_CTG8  25
754                                  Xq13.3  25
755                                12q21.32  24
756                                 13q21.2  24
757                                 13q22.1  24
758                                20p11.22  24
759                                 4q31.22  24
760                      CHR_HSCHR15_5_CTG8  24
761                      CHR_HSCHR22_1_CTG3  24
762                     CHR_HSCHR2_6_CTG7_2  24
763                     CHR_HSCHR5_1_CTG1_1  24
764                                  Xp21.2  24
765                                 10p15.2  23
766                                 17q21.1  23
767                                  3q22.2  23
768                                  4q22.3  23
769                                  5q22.2  23
770                        CHR_HG2030_PATCH  23
771                         CHR_HG708_PATCH  23
772             CHR_HSCHR19LRC_LRC_I_CTG3_1  23
773             CHR_HSCHR19LRC_LRC_T_CTG3_1  23
774                     CHR_HSCHR4_11_CTG12  23
775                       CHR_HSCHR8_3_CTG7  23
776                                13q21.32  22
777                                 14q13.1  22
778                                 18q22.2  22
779                                  3p12.2  22
780                                  3q27.2  22
781                                  5q14.2  22
782                                  8p11.1  22
783                      CHR_HSCHR15_1_CTG1  22
784                       CHR_HSCHR4_1_CTG9  22
785                     CHR_HSCHR7_3_CTG4_4  22
786                                 16q11.2  21
787                                 1q42.11  21
788                                  3p11.1  21
789                                  3p12.1  21
790                                  6p24.1  21
791                                  7p21.2  21
792                                 9q21.31  21
793                        CHR_HG2002_PATCH  21
794                        CHR_HG2066_PATCH  21
795          CHR_HG2246_HG2248_HG2276_PATCH  21
796             CHR_HSCHR19LRC_LRC_J_CTG3_1  21
797                       CHR_HSCHR8_3_CTG1  21
798                                  Xq11.2  21
799                                12q24.12  20
800                                 13q32.2  20
801                                 4p15.31  20
802                        CHR_HG2198_PATCH  20
803                         CHR_HG926_PATCH  20
804                     CHR_HSCHR17_10_CTG4  20
805             CHR_HSCHR19LRC_LRC_S_CTG3_1  20
806                                 13q22.2  19
807                                 14q22.2  19
808                                 20p11.1  19
809                                  2q37.2  19
810                                  4q32.2  19
811                        CHR_HG2046_PATCH  19
812                        CHR_HG2513_PATCH  19
813        CHR_HSCHR19KIR_FH15_B_HAP_CTG3_1  19
814                       CHR_HSCHR1_5_CTG3  19
815                                 12p11.1  18
816                                 16q22.3  18
817                                  4p16.2  18
818                                  5q11.1  18
819                                  6p11.2  18
820                        CHR_HG2419_PATCH  18
821        CHR_HSCHR19KIR_FH05_B_HAP_CTG3_1  18
822                                  2q22.2  17
823                                  2q23.1  17
824                                  4q34.2  17
825                                  6q16.2  17
826                                  8q23.2  17
827                                 8q24.11  17
828                        CHR_HG2087_PATCH  17
829                        CHR_HG2217_PATCH  17
830                         CHR_HG545_PATCH  17
831         CHR_HSCHR19KIR_CA01-TB04_CTG3_1  17
832      CHR_HSCHR19KIR_FH13_BA2_HAP_CTG3_1  17
833                       CHR_HSCHR1_2_CTG3  17
834                                10p12.33  16
835                                10q26.12  16
836                                 13q13.2  16
837                                18p11.23  16
838                                   19q11  16
839                                  5p14.2  16
840                                  7p12.2  16
841                        CHR_HG1362_PATCH  16
842              CHR_HG142_HG150_NOVEL_TEST  16
843                          CHR_HG28_PATCH  16
844                      CHR_HSCHR11_1_CTG8  16
845         CHR_HSCHR19KIR_CA01-TB01_CTG3_1  16
846                    CHR_HSCHR19_3_CTG3_1  16
847                       CHR_HSCHR8_8_CTG1  16
848                                  Xq21.2  16
849                                  Xq27.2  16
850                                 12p12.2  15
851                                 17q11.1  15
852                                 3q13.32  15
853                                 8q24.23  15
854                                  9p22.2  15
855                        CHR_HG2114_PATCH  15
856                        CHR_HG2499_PATCH  15
857                      CHR_HSCHR11_1_CTG7  15
858       CHR_HSCHR19KIR_0019-4656-B_CTG3_1  15
859      CHR_HSCHR19KIR_FH08_BAX_HAP_CTG3_1  15
860                       CHR_HSCHR1_4_CTG3  15
861                                 13q33.2  14
862                                  4q21.3  14
863                                    9q12  14
864                        CHR_HG2021_PATCH  14
865                         CHR_HG439_PATCH  14
866                      CHR_HSCHR15_3_CTG3  14
867                      CHR_HSCHR16_3_CTG1  14
868         CHR_HSCHR19KIR_7191059-2_CTG3_1  14
869        CHR_HSCHR19KIR_FH15_A_HAP_CTG3_1  14
870        CHR_HSCHR19KIR_G248_A_HAP_CTG3_1  14
871     CHR_HSCHR19KIR_GRC212_AB_HAP_CTG3_1  14
872     CHR_HSCHR19KIR_LUCE_BDEL_HAP_CTG3_1  14
873    CHR_HSCHR19KIR_T7526_BDEL_HAP_CTG3_1  14
874                       CHR_HSCHR1_1_CTG3  14
875                      CHR_HSCHR1_1_CTG31  14
876                    CHR_HSCHR1_5_CTG32_1  14
877                                 17q25.2  13
878                                20q13.11  13
879                                22q13.32  13
880                                 3q13.11  13
881                                  6q11.1  13
882                                 6q22.32  13
883                                  7p22.2  13
884                                 9q34.12  13
885                    CHR_HSCHR11_2_CTG1_1  13
886       CHR_HSCHR19KIR_502960008-1_CTG3_1  13
887       CHR_HSCHR19KIR_502960008-2_CTG3_1  13
888         CHR_HSCHR19KIR_7191059-1_CTG3_1  13
889  CHR_HSCHR19KIR_ABC08_AB_HAP_T_P_CTG3_1  13
890       CHR_HSCHR19KIR_CA01-TA01_1_CTG3_1  13
891       CHR_HSCHR19KIR_CA01-TA01_2_CTG3_1  13
892        CHR_HSCHR19KIR_FH05_A_HAP_CTG3_1  13
893        CHR_HSCHR19KIR_FH06_A_HAP_CTG3_1  13
894      CHR_HSCHR19KIR_FH06_BA1_HAP_CTG3_1  13
895        CHR_HSCHR19KIR_FH13_A_HAP_CTG3_1  13
896        CHR_HSCHR19KIR_G085_A_HAP_CTG3_1  13
897      CHR_HSCHR19KIR_G085_BA1_HAP_CTG3_1  13
898            CHR_HSCHR19KIR_HG2394_CTG3_1  13
899         CHR_HSCHR19KIR_RSH_A_HAP_CTG3_1  13
900       CHR_HSCHR19KIR_RSH_BA2_HAP_CTG3_1  13
901       CHR_HSCHR19KIR_T7526_A_HAP_CTG3_1  13
902                      CHR_HSCHR4_6_CTG12  13
903                                  Xq11.1  13
904                                  3q12.2  12
905                                  5q21.2  12
906                                  8q12.2  12
907                    CHR_HG151_NOVEL_TEST  12
908                      CHR_HSCHR11_1_CTG6  12
909                      CHR_HSCHR15_2_CTG3  12
910                      CHR_HSCHR17_1_CTG4  12
911       CHR_HSCHR19KIR_0019-4656-A_CTG3_1  12
912      CHR_HSCHR19KIR_ABC08_A1_HAP_CTG3_1  12
913        CHR_HSCHR19KIR_FH08_A_HAP_CTG3_1  12
914         CHR_HSCHR19KIR_RP5_B_HAP_CTG3_1  12
915                       CHR_HSCHR3_5_CTG1  12
916                       CHR_HSCHR3_9_CTG3  12
917                                13q14.12  11
918                                19q13.13  11
919                                    3p23  11
920                                  6q14.2  11
921                        CHR_HG1277_PATCH  11
922                        CHR_HG1309_PATCH  11
923                        CHR_HG1398_PATCH  11
924                        CHR_HG2263_PATCH  11
925                    CHR_HSCHR11_1_CTG1_2  11
926                      CHR_HSCHR15_1_CTG3  11
927                      CHR_HSCHR17_1_CTG1  11
928      CHR_HSCHR19KIR_G248_BA2_HAP_CTG3_1  11
929                      CHR_HSCHR19_1_CTG2  11
930                      CHR_HSCHR19_3_CTG2  11
931                      CHR_HSCHR22_3_CTG1  11
932                                 Xq21.32  11
933                                  2p11.1  10
934                                  3p26.2  10
935                        CHR_HG2057_PATCH  10
936                        CHR_HG2266_PATCH  10
937                        CHR_HG2334_PATCH  10
938                      CHR_HSCHR10_1_CTG2  10
939                      CHR_HSCHR17_1_CTG2  10
940  CHR_HSCHR19KIR_ABC08_AB_HAP_C_P_CTG3_1  10
941    CHR_HSCHR19KIR_GRC212_BA1_HAP_CTG3_1  10
942            CHR_HSCHR19KIR_HG2393_CTG3_1  10
943        CHR_HSCHR19KIR_LUCE_A_HAP_CTG3_1  10
944                      CHR_HSCHR1_2_CTG31  10
945                       CHR_HSCHR5_8_CTG1  10
946                       CHR_HSCHR7_2_CTG1  10
947                                 18q11.1   9
948                                 22p11.2   9
949                                  3p11.2   9
950                        CHR_HG1832_PATCH   9
951                        CHR_HG2058_PATCH   9
952                        CHR_HG2095_PATCH   9
953                        CHR_HG2115_PATCH   9
954                        CHR_HG2232_PATCH   9
955           CHR_HG2285_HG106_HG2252_PATCH   9
956                        CHR_HG2291_PATCH   9
957                        CHR_HG2525_PATCH   9
958                      CHR_HSCHR11_1_CTG5   9
959                      CHR_HSCHR11_2_CTG8   9
960                      CHR_HSCHR12_1_CTG1   9
961                      CHR_HSCHR13_1_CTG3   9
962                      CHR_HSCHR14_1_CTG1   9
963                      CHR_HSCHR15_3_CTG8   9
964                      CHR_HSCHR17_6_CTG4   9
965      CHR_HSCHR19KIR_0010-5217-AB_CTG3_1   9
966            CHR_HSCHR19KIR_HG2396_CTG3_1   9
967                      CHR_HSCHR19_2_CTG2   9
968               CHR_HSCHR1_ALT2_1_CTG32_1   9
969                      CHR_HSCHR22_1_CTG6   9
970                      CHR_HSCHR22_2_CTG1   9
971                      CHR_HSCHR2_3_CTG15   9
972                     CHR_HSCHR2_8_CTG7_2   9
973                       CHR_HSCHR6_1_CTG8   9
974                     CHR_HSCHR7_2_CTG4_4   9
975                       CHR_HSCHR8_9_CTG1   9
976                       CHR_HSCHR9_1_CTG5   9
977                                 15q22.1   8
978                                  2q23.2   8
979                                  3q11.1   8
980                        CHR_HG1311_PATCH   8
981                        CHR_HG1395_PATCH   8
982                        CHR_HG1535_PATCH   8
983                        CHR_HG2111_PATCH   8
984                        CHR_HG2121_PATCH   8
985                      CHR_HSCHR17_2_CTG2   8
986                      CHR_HSCHR17_5_CTG4   8
987              CHR_HSCHR19KIR_CA04_CTG3_1   8
988                    CHR_HSCHR1_3_CTG32_1   8
989                      CHR_HSCHR1_4_CTG31   8
990                       CHR_HSCHR1_6_CTG3   8
991                      CHR_HSCHR22_1_CTG1   8
992                      CHR_HSCHR22_4_CTG1   8
993                      CHR_HSCHR22_7_CTG1   8
994                       CHR_HSCHR3_1_CTG1   8
995                       CHR_HSCHR5_2_CTG5   8
996                       CHR_HSCHR5_3_CTG5   8
997                       CHR_HSCHR6_1_CTG4   8
998                       CHR_HSCHR7_1_CTG1   8
999                     CHR_HSCHR7_1_CTG4_4   8
1000                      CHR_HSCHR8_5_CTG7   8
1001                                11p14.2   7
1002                                14q31.2   7
1003                                 2q36.2   7
1004                                 4q22.2   7
1005                                 6q23.1   7
1006                       CHR_HG1485_PATCH   7
1007                        CHR_HG986_PATCH   7
1008                     CHR_HSCHR10_1_CTG1   7
1009                     CHR_HSCHR10_1_CTG4   7
1010                   CHR_HSCHR11_1_CTG3_1   7
1011                     CHR_HSCHR12_4_CTG2   7
1012                     CHR_HSCHR16_5_CTG1   7
1013                   CHR_HSCHR16_5_CTG3_1   7
1014                       CHR_HSCHR16_CTG2   7
1015                   CHR_HSCHR1_2_CTG32_1   7
1016                     CHR_HSCHR22_8_CTG1   7
1017                      CHR_HSCHR2_2_CTG7   7
1018                      CHR_HSCHR3_1_CTG3   7
1019                    CHR_HSCHR3_4_CTG2_1   7
1020                      CHR_HSCHR3_5_CTG3   7
1021                      CHR_HSCHR6_1_CTG5   7
1022                      CHR_HSCHR7_1_CTG6   7
1023                      CHR_HSCHR8_4_CTG7   7
1024                      CHR_HSCHRX_1_CTG3   7
1025                             KI270727.1   7
1026                                Xp22.32   7
1027                                 1p31.2   6
1028                                3p21.33   6
1029                                 7p15.1   6
1030                       CHR_HG2072_PATCH   6
1031                       CHR_HG2191_PATCH   6
1032                       CHR_HG2213_PATCH   6
1033                       CHR_HG2412_PATCH   6
1034                   CHR_HSCHR12_1_CTG2_1   6
1035                     CHR_HSCHR14_8_CTG1   6
1036                   CHR_HSCHR18_1_CTG1_1   6
1037                   CHR_HSCHR18_3_CTG2_1   6
1038                     CHR_HSCHR19_5_CTG2   6
1039                      CHR_HSCHR1_8_CTG3   6
1040                     CHR_HSCHR20_1_CTG3   6
1041                   CHR_HSCHR21_4_CTG1_1   6
1042                     CHR_HSCHR22_5_CTG1   6
1043                     CHR_HSCHR22_6_CTG1   6
1044                      CHR_HSCHR3_3_CTG3   6
1045                      CHR_HSCHR3_4_CTG3   6
1046                      CHR_HSCHR3_6_CTG3   6
1047                      CHR_HSCHR3_7_CTG3   6
1048                      CHR_HSCHR3_8_CTG3   6
1049                     CHR_HSCHR4_7_CTG12   6
1050                     CHR_HSCHR4_9_CTG12   6
1051                      CHR_HSCHR5_3_CTG1   6
1052                      CHR_HSCHR8_1_CTG1   6
1053                      CHR_HSCHR8_7_CTG1   6
1054                             KI270728.1   6
1055                                 7q22.2   5
1056                                   9q11   5
1057                        CHR_HG126_PATCH   5
1058                       CHR_HG1445_PATCH   5
1059                       CHR_HG2236_PATCH   5
1060                     CHR_HSCHR10_1_CTG3   5
1061                     CHR_HSCHR11_3_CTG1   5
1062                     CHR_HSCHR13_1_CTG1   5
1063                   CHR_HSCHR16_4_CTG3_1   5
1064                     CHR_HSCHR17_2_CTG1   5
1065                     CHR_HSCHR18_2_CTG2   5
1066                     CHR_HSCHR1_3_CTG31   5
1067                   CHR_HSCHR21_2_CTG1_1   5
1068                     CHR_HSCHR21_5_CTG2   5
1069                   CHR_HSCHR21_6_CTG1_1   5
1070                     CHR_HSCHR2_1_CTG15   5
1071                     CHR_HSCHR2_2_CTG15   5
1072                    CHR_HSCHR3_6_CTG2_1   5
1073                    CHR_HSCHR4_12_CTG12   5
1074                      CHR_HSCHR6_1_CTG2   5
1075                      CHR_HSCHR7_3_CTG6   5
1076                      CHR_HSCHR8_1_CTG6   5
1077                      CHR_HSCHR8_2_CTG7   5
1078                      CHR_HSCHRX_2_CTG3   5
1079                               15q22.33   4
1080                        CHR_HG107_PATCH   4
1081                       CHR_HG2060_PATCH   4
1082                       CHR_HG2104_PATCH   4
1083                       CHR_HG2235_PATCH   4
1084                       CHR_HG2471_PATCH   4
1085                   CHR_HSCHR12_3_CTG2_1   4
1086                   CHR_HSCHR12_9_CTG2_1   4
1087                   CHR_HSCHR16_2_CTG3_1   4
1088                     CHR_HSCHR16_4_CTG1   4
1089                     CHR_HSCHR17_1_CTG9   4
1090                     CHR_HSCHR17_3_CTG2   4
1091                CHR_HSCHR18_ALT2_CTG2_1   4
1092                   CHR_HSCHR21_3_CTG1_1   4
1093                     CHR_HSCHR22_1_CTG2   4
1094                     CHR_HSCHR22_1_CTG4   4
1095                     CHR_HSCHR22_1_CTG5   4
1096                      CHR_HSCHR2_1_CTG1   4
1097                      CHR_HSCHR2_1_CTG7   4
1098                    CHR_HSCHR2_1_CTG7_2   4
1099                    CHR_HSCHR2_3_CTG7_2   4
1100                      CHR_HSCHR3_2_CTG3   4
1101                    CHR_HSCHR3_9_CTG2_1   4
1102                      CHR_HSCHR4_1_CTG4   4
1103                     CHR_HSCHR4_3_CTG12   4
1104                      CHR_HSCHR5_2_CTG1   4
1105                      CHR_HSCHR5_4_CTG1   4
1106                      CHR_HSCHR5_5_CTG1   4
1107                      CHR_HSCHR5_6_CTG1   4
1108                      CHR_HSCHR6_1_CTG9   4
1109                      CHR_HSCHR8_4_CTG1   4
1110                      CHR_HSCHR9_1_CTG3   4
1111                             GL000220.1   4
1112                             KI270713.1   4
1113                             KI270721.1   4
1114                             KI270733.1   4
1115                             KI270734.1   4
1116                                3p21.32   3
1117                       CHR_HG1298_PATCH   3
1118                       CHR_HG1320_PATCH   3
1119                       CHR_HG1524_PATCH   3
1120                       CHR_HG1708_PATCH   3
1121                       CHR_HG2063_PATCH   3
1122                       CHR_HG2133_PATCH   3
1123                       CHR_HG2247_PATCH   3
1124                CHR_HG2288_HG2289_PATCH   3
1125                       CHR_HG2442_PATCH   3
1126                       CHR_HG2509_PATCH   3
1127                       CHR_HG2510_PATCH   3
1128                       CHR_HG2511_PATCH   3
1129                        CHR_HG699_PATCH   3
1130                        CHR_HG705_PATCH   3
1131                        CHR_HG721_PATCH   3
1132                     CHR_HSCHR11_2_CTG1   3
1133                   CHR_HSCHR12_2_CTG2_1   3
1134                   CHR_HSCHR12_4_CTG2_1   3
1135                   CHR_HSCHR12_5_CTG2_1   3
1136                   CHR_HSCHR12_6_CTG2_1   3
1137                     CHR_HSCHR13_1_CTG5   3
1138                     CHR_HSCHR14_2_CTG1   3
1139                     CHR_HSCHR15_2_CTG8   3
1140                   CHR_HSCHR16_1_CTG3_1   3
1141                     CHR_HSCHR17_3_CTG4   3
1142                   CHR_HSCHR18_2_CTG2_1   3
1143                   CHR_HSCHR19_1_CTG3_1   3
1144                   CHR_HSCHR19_2_CTG3_1   3
1145                     CHR_HSCHR1_1_CTG11   3
1146                     CHR_HSCHR20_1_CTG1   3
1147                     CHR_HSCHR20_1_CTG4   3
1148                      CHR_HSCHR2_1_CTG5   3
1149                      CHR_HSCHR2_2_CTG1   3
1150                      CHR_HSCHR2_4_CTG1   3
1151                    CHR_HSCHR3_1_CTG2_1   3
1152                    CHR_HSCHR3_2_CTG2_1   3
1153                      CHR_HSCHR3_4_CTG1   3
1154                    CHR_HSCHR3_8_CTG2_1   3
1155                     CHR_HSCHR4_1_CTG12   3
1156                     CHR_HSCHR4_5_CTG12   3
1157                    CHR_HSCHR5_4_CTG1_1   3
1158                      CHR_HSCHR7_3_CTG1   3
1159                      CHR_HSCHR8_2_CTG1   3
1160                      CHR_HSCHR9_1_CTG2   3
1161                                   Yq12   3
1162                               15q22.32   2
1163                                 6q22.2   2
1164                                8q21.12   2
1165                       CHR_HG1384_PATCH   2
1166                       CHR_HG2022_PATCH   2
1167                       CHR_HG2047_PATCH   2
1168                       CHR_HG2067_PATCH   2
1169                       CHR_HG2088_PATCH   2
1170                       CHR_HG2116_PATCH   2
1171                       CHR_HG2128_PATCH   2
1172                       CHR_HG2233_PATCH   2
1173                       CHR_HG2249_PATCH   2
1174                       CHR_HG2512_PATCH   2
1175                     CHR_HSCHR17_8_CTG4   2
1176                     CHR_HSCHR17_9_CTG4   2
1177                     CHR_HSCHR18_1_CTG1   2
1178                   CHR_HSCHR18_1_CTG2_1   2
1179                   CHR_HSCHR18_5_CTG1_1   2
1180               CHR_HSCHR18_ALT21_CTG2_1   2
1181                      CHR_HSCHR1_9_CTG3   2
1182                     CHR_HSCHR20_1_CTG2   2
1183                   CHR_HSCHR21_8_CTG1_1   2
1184                    CHR_HSCHR2_7_CTG7_2   2
1185                    CHR_HSCHR3_5_CTG2_1   2
1186                     CHR_HSCHR4_8_CTG12   2
1187                      CHR_HSCHR5_1_CTG5   2
1188                      CHR_HSCHR6_1_CTG7   2
1189                      CHR_HSCHR6_8_CTG1   2
1190                      CHR_HSCHR8_1_CTG7   2
1191                      CHR_HSCHR8_5_CTG1   2
1192                      CHR_HSCHR8_6_CTG1   2
1193                      CHR_HSCHR8_7_CTG7   2
1194                      CHR_HSCHR9_1_CTG4   2
1195                      CHR_HSCHR9_1_CTG6   2
1196                             GL000194.1   2
1197                             GL000195.1   2
1198                             GL000213.1   2
1199                             KI270442.1   2
1200                             KI270726.1   2
1201                             KI270731.1   2
1202                                  12q11   1
1203                                14p11.2   1
1204                                 6q11.2   1
1205                                8q11.22   1
1206                       CHR_HG1531_PATCH   1
1207                       CHR_HG1651_PATCH   1
1208                       CHR_HG2062_PATCH   1
1209                       CHR_HG2239_PATCH   1
1210                     CHR_HSCHR10_1_CTG6   1
1211                     CHR_HSCHR12_5_CTG2   1
1212                   CHR_HSCHR12_8_CTG2_1   1
1213                     CHR_HSCHR14_9_CTG1   1
1214                    CHR_HSCHR17_11_CTG4   1
1215                    CHR_HSCHR17_12_CTG4   1
1216                     CHR_HSCHR17_2_CTG4   1
1217                   CHR_HSCHR18_2_CTG1_1   1
1218                     CHR_HSCHR19_4_CTG2   1
1219                   CHR_HSCHR1_1_CTG32_1   1
1220                      CHR_HSCHR1_3_CTG3   1
1221                    CHR_HSCHR2_2_CTG7_2   1
1222                      CHR_HSCHR2_3_CTG1   1
1223                      CHR_HSCHR3_3_CTG1   1
1224                      CHR_HSCHR4_1_CTG6   1
1225                     CHR_HSCHR4_2_CTG12   1
1226                      CHR_HSCHR4_2_CTG4   1
1227                     CHR_HSCHR4_4_CTG12   1
1228                      CHR_HSCHR5_1_CTG1   1
1229                      CHR_HSCHR5_7_CTG1   1
1230                      CHR_HSCHR6_1_CTG3   1
1231                      CHR_HSCHR6_1_CTG6   1
1232                      CHR_HSCHR7_1_CTG7   1
1233                      CHR_HSCHR7_2_CTG7   1
1234                      CHR_HSCHR9_1_CTG1   1
1235                     CHR_HSCHRX_2_CTG12   1
1236                             GL000009.2   1
1237                             GL000205.2   1
1238                             GL000216.2   1
1239                             GL000218.1   1
1240                             GL000219.1   1
1241                             GL000225.1   1
1242                             KI270711.1   1
1243                             KI270744.1   1
1244                             KI270750.1   1
Code
anno_gene %>% count(cytoband) %>% arrange(desc(n)) %>% summary()
   cytoband               n         
 Length:1244        Min.   :  1.00  
 Class :character   1st Qu.: 10.00  
 Mode  :character   Median : 39.00  
                    Mean   : 55.71  
                    3rd Qu.: 78.00  
                    Max.   :457.00  

Reuse

© HakyImLab and Listed Authors - CC BY 4.0 for Text and figures - MIT for code