在R中使用GenomeInfoDb获取染色体信息

发表于 | 分类于 | | 热度 °C

在生物信息分析中，经常需要用到染色体的信息，可以使用GenomeInfoDb来获取，如下：

一、获取human的染色体信息

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library(GenomeInfoDb)

> hg_chrs = fetchExtendedChromInfoFromUCSC('hg38')
> hg_chrs
           UCSC_seqlevel UCSC_seqlength circular          NCBI_seqlevel       SequenceRole GenBankAccn
1                   chr1      248956422    FALSE                      1 assembled-molecule  CM000663.2
2                   chr2      242193529    FALSE                      2 assembled-molecule  CM000664.2
3                   chr3      198295559    FALSE                      3 assembled-molecule  CM000665.2
4                   chr4      190214555    FALSE                      4 assembled-molecule  CM000666.2
5                   chr5      181538259    FALSE                      5 assembled-molecule  CM000667.2
6                   chr6      170805979    FALSE                      6 assembled-molecule  CM000668.2
7                   chr7      159345973    FALSE                      7 assembled-molecule  CM000669.2
8                   chr8      145138636    FALSE                      8 assembled-molecule  CM000670.2
9                   chr9      138394717    FALSE                      9 assembled-molecule  CM000671.2
10                 chr10      133797422    FALSE                     10 assembled-molecule  CM000672.2
11                 chr11      135086622    FALSE                     11 assembled-molecule  CM000673.2
12                 chr12      133275309    FALSE                     12 assembled-molecule  CM000674.2
13                 chr13      114364328    FALSE                     13 assembled-molecule  CM000675.2
14                 chr14      107043718    FALSE                     14 assembled-molecule  CM000676.2
15                 chr15      101991189    FALSE                     15 assembled-molecule  CM000677.2
16                 chr16       90338345    FALSE                     16 assembled-molecule  CM000678.2
17                 chr17       83257441    FALSE                     17 assembled-molecule  CM000679.2
18                 chr18       80373285    FALSE                     18 assembled-molecule  CM000680.2
19                 chr19       58617616    FALSE                     19 assembled-molecule  CM000681.2
20                 chr20       64444167    FALSE                     20 assembled-molecule  CM000682.2
21                 chr21       46709983    FALSE                     21 assembled-molecule  CM000683.2
22                 chr22       50818468    FALSE                     22 assembled-molecule  CM000684.2
23                  chrX      156040895    FALSE                      X assembled-molecule  CM000685.2
24                  chrY       57227415    FALSE                      Y assembled-molecule  CM000686.2
25                  chrM          16569     TRUE                     MT assembled-molecule    J01415.2
26   chr1_GL383518v1_alt         182439    FALSE         HSCHR1_1_CTG31       alt-scaffold  GL383518.1
27   chr1_GL383519v1_alt         110268    FALSE         HSCHR1_2_CTG31       alt-scaffold  GL383519.1
28   chr1_GL383520v2_alt         366580    FALSE         HSCHR1_3_CTG31       alt-scaffold  GL383520.2
29   chr1_KI270759v1_alt         425601    FALSE       HSCHR1_1_CTG32_1       alt-scaffold  KI270759.1
30   chr1_KI270760v1_alt         109528    FALSE         HSCHR1_1_CTG11       alt-scaffold  KI270760.1
31   chr1_KI270761v1_alt         165834    FALSE       HSCHR1_2_CTG32_1       alt-scaffold  KI270761.1
32   chr1_KI270762v1_alt         354444    FALSE          HSCHR1_1_CTG3       alt-scaffold  KI270762.1
33   chr1_KI270763v1_alt         911658    FALSE       HSCHR1_3_CTG32_1       alt-scaffold  KI270763.1
34   chr1_KI270764v1_alt          50258    FALSE       HSCHR1_4_CTG32_1       alt-scaffold  KI270764.1
35   chr1_KI270765v1_alt         185285    FALSE         HSCHR1_4_CTG31       alt-scaffold  KI270765.1
36   chr1_KI270766v1_alt         256271    FALSE          HSCHR1_2_CTG3       alt-scaffold  KI270766.1
37   chr1_KI270892v1_alt         162212    FALSE  HSCHR1_ALT2_1_CTG32_1       alt-scaffold  KI270892.1
38   chr2_GL383521v1_alt         143390    FALSE          HSCHR2_1_CTG5       alt-scaffold  GL383521.1
39   chr2_GL383522v1_alt         123821    FALSE        HSCHR2_1_CTG7_2       alt-scaffold  GL383522.1
40   chr2_GL582966v2_alt          96131    FALSE        HSCHR2_2_CTG7_2       alt-scaffold  GL582966.2
41   chr2_KI270767v1_alt         161578    FALSE         HSCHR2_1_CTG15       alt-scaffold  KI270767.1
42   chr2_KI270768v1_alt         110099    FALSE        HSCHR2_3_CTG7_2       alt-scaffold  KI270768.1
43   chr2_KI270769v1_alt         120616    FALSE          HSCHR2_1_CTG1       alt-scaffold  KI270769.1
44   chr2_KI270770v1_alt         136240    FALSE          HSCHR2_2_CTG1       alt-scaffold  KI270770.1
45   chr2_KI270771v1_alt         110395    FALSE        HSCHR2_4_CTG7_2       alt-scaffold  KI270771.1
46   chr2_KI270772v1_alt         133041    FALSE          HSCHR2_1_CTG7       alt-scaffold  KI270772.1
47   chr2_KI270773v1_alt          70887    FALSE          HSCHR2_3_CTG1       alt-scaffold  KI270773.1
48   chr2_KI270774v1_alt         223625    FALSE          HSCHR2_4_CTG1       alt-scaffold  KI270774.1
49   chr2_KI270775v1_alt         138019    FALSE        HSCHR2_5_CTG7_2       alt-scaffold  KI270775.1
50   chr2_KI270776v1_alt         174166    FALSE         HSCHR2_3_CTG15       alt-scaffold  KI270776.1
51   chr2_KI270893v1_alt         161218    FALSE         HSCHR2_2_CTG15       alt-scaffold  KI270893.1
52   chr2_KI270894v1_alt         214158    FALSE          HSCHR2_2_CTG7       alt-scaffold  KI270894.1
53   chr3_GL383526v1_alt         180671    FALSE        HSCHR3_1_CTG2_1       alt-scaffold  GL383526.1
54   chr3_JH636055v2_alt         173151    FALSE          HSCHR3_1_CTG1       alt-scaffold  JH636055.2
55   chr3_KI270777v1_alt         173649    FALSE        HSCHR3_2_CTG2_1       alt-scaffold  KI270777.1
56   chr3_KI270778v1_alt         248252    FALSE        HSCHR3_3_CTG2_1       alt-scaffold  KI270778.1
57   chr3_KI270779v1_alt         205312    FALSE          HSCHR3_1_CTG3       alt-scaffold  KI270779.1
58   chr3_KI270780v1_alt         224108    FALSE        HSCHR3_4_CTG2_1       alt-scaffold  KI270780.1
59   chr3_KI270781v1_alt         113034    FALSE        HSCHR3_5_CTG2_1       alt-scaffold  KI270781.1
60   chr3_KI270782v1_alt         162429    FALSE          HSCHR3_2_CTG3       alt-scaffold  KI270782.1
61   chr3_KI270783v1_alt         109187    FALSE          HSCHR3_3_CTG1       alt-scaffold  KI270783.1
62   chr3_KI270784v1_alt         184404    FALSE          HSCHR3_9_CTG3       alt-scaffold  KI270784.1
63   chr3_KI270895v1_alt         162896    FALSE          HSCHR3_3_CTG3       alt-scaffold  KI270895.1
64   chr3_KI270924v1_alt         166540    FALSE          HSCHR3_4_CTG3       alt-scaffold  KI270924.1
65   chr3_KI270934v1_alt         163458    FALSE          HSCHR3_5_CTG3       alt-scaffold  KI270934.1
66   chr3_KI270935v1_alt         197351    FALSE          HSCHR3_6_CTG3       alt-scaffold  KI270935.1
67   chr3_KI270936v1_alt         164170    FALSE          HSCHR3_7_CTG3       alt-scaffold  KI270936.1
68   chr3_KI270937v1_alt         165607    FALSE          HSCHR3_8_CTG3       alt-scaffold  KI270937.1
69   chr4_GL000257v2_alt         586476    FALSE          HSCHR4_1_CTG9       alt-scaffold  GL000257.2
70   chr4_GL383527v1_alt         164536    FALSE         HSCHR4_1_CTG12       alt-scaffold  GL383527.1
71   chr4_GL383528v1_alt         376187    FALSE          HSCHR4_1_CTG6       alt-scaffold  GL383528.1
72   chr4_KI270785v1_alt         119912    FALSE         HSCHR4_2_CTG12       alt-scaffold  KI270785.1
73   chr4_KI270786v1_alt         244096    FALSE         HSCHR4_3_CTG12       alt-scaffold  KI270786.1
74   chr4_KI270787v1_alt         111943    FALSE        HSCHR4_1_CTG8_1       alt-scaffold  KI270787.1
75   chr4_KI270788v1_alt         158965    FALSE         HSCHR4_4_CTG12       alt-scaffold  KI270788.1
76   chr4_KI270789v1_alt         205944    FALSE         HSCHR4_5_CTG12       alt-scaffold  KI270789.1
77   chr4_KI270790v1_alt         220246    FALSE          HSCHR4_1_CTG4       alt-scaffold  KI270790.1
78   chr4_KI270896v1_alt         378547    FALSE         HSCHR4_6_CTG12       alt-scaffold  KI270896.1
79   chr4_KI270925v1_alt         555799    FALSE         HSCHR4_7_CTG12       alt-scaffold  KI270925.1
80   chr5_GL339449v2_alt        1612928    FALSE        HSCHR5_2_CTG1_1       alt-scaffold  GL339449.2
81   chr5_GL383530v1_alt         101241    FALSE        HSCHR5_3_CTG1_1       alt-scaffold  GL383530.1
82   chr5_GL383531v1_alt         173459    FALSE          HSCHR5_1_CTG5       alt-scaffold  GL383531.1
83   chr5_GL383532v1_alt          82728    FALSE          HSCHR5_1_CTG1       alt-scaffold  GL383532.1
84   chr5_GL949742v1_alt         226852    FALSE          HSCHR5_2_CTG1       alt-scaffold  GL949742.1
85   chr5_KI270791v1_alt         195710    FALSE          HSCHR5_3_CTG1       alt-scaffold  KI270791.1
86   chr5_KI270792v1_alt         179043    FALSE          HSCHR5_4_CTG1       alt-scaffold  KI270792.1
87   chr5_KI270793v1_alt         126136    FALSE          HSCHR5_5_CTG1       alt-scaffold  KI270793.1
88   chr5_KI270794v1_alt         164558    FALSE          HSCHR5_6_CTG1       alt-scaffold  KI270794.1
89   chr5_KI270795v1_alt         131892    FALSE          HSCHR5_2_CTG5       alt-scaffold  KI270795.1
90   chr5_KI270796v1_alt         172708    FALSE        HSCHR5_4_CTG1_1       alt-scaffold  KI270796.1
91   chr5_KI270897v1_alt        1144418    FALSE        HSCHR5_1_CTG1_1       alt-scaffold  KI270897.1
92   chr5_KI270898v1_alt         130957    FALSE          HSCHR5_3_CTG5       alt-scaffold  KI270898.1
93   chr6_GL000250v2_alt        4672374    FALSE    HSCHR6_MHC_APD_CTG1       alt-scaffold  GL000250.2
94   chr6_GL000251v2_alt        4795265    FALSE    HSCHR6_MHC_COX_CTG1       alt-scaffold  GL000251.2
95   chr6_GL000252v2_alt        4604811    FALSE    HSCHR6_MHC_DBB_CTG1       alt-scaffold  GL000252.2
96   chr6_GL000253v2_alt        4677643    FALSE   HSCHR6_MHC_MANN_CTG1       alt-scaffold  GL000253.2
97   chr6_GL000254v2_alt        4827813    FALSE    HSCHR6_MHC_MCF_CTG1       alt-scaffold  GL000254.2
98   chr6_GL000255v2_alt        4606388    FALSE    HSCHR6_MHC_QBL_CTG1       alt-scaffold  GL000255.2
99   chr6_GL000256v2_alt        4929269    FALSE   HSCHR6_MHC_SSTO_CTG1       alt-scaffold  GL000256.2
100  chr6_GL383533v1_alt         124736    FALSE          HSCHR6_1_CTG2       alt-scaffold  GL383533.1
101  chr6_KB021644v2_alt         185823    FALSE          HSCHR6_1_CTG3       alt-scaffold  KB021644.2
102  chr6_KI270758v1_alt          76752    FALSE          HSCHR6_8_CTG1       alt-scaffold  KI270758.1
103  chr6_KI270797v1_alt         197536    FALSE          HSCHR6_1_CTG4       alt-scaffold  KI270797.1
104  chr6_KI270798v1_alt         271782    FALSE          HSCHR6_1_CTG5       alt-scaffold  KI270798.1
105  chr6_KI270799v1_alt         152148    FALSE          HSCHR6_1_CTG6       alt-scaffold  KI270799.1
106  chr6_KI270800v1_alt         175808    FALSE          HSCHR6_1_CTG7       alt-scaffold  KI270800.1
107  chr6_KI270801v1_alt         870480    FALSE          HSCHR6_1_CTG8       alt-scaffold  KI270801.1
108  chr6_KI270802v1_alt          75005    FALSE          HSCHR6_1_CTG9       alt-scaffold  KI270802.1
109  chr7_GL383534v2_alt         119183    FALSE          HSCHR7_1_CTG6       alt-scaffold  GL383534.2
110  chr7_KI270803v1_alt        1111570    FALSE          HSCHR7_2_CTG6       alt-scaffold  KI270803.1
111  chr7_KI270804v1_alt         157952    FALSE          HSCHR7_1_CTG1       alt-scaffold  KI270804.1
112  chr7_KI270805v1_alt         209988    FALSE          HSCHR7_1_CTG7       alt-scaffold  KI270805.1
113  chr7_KI270806v1_alt         158166    FALSE        HSCHR7_1_CTG4_4       alt-scaffold  KI270806.1
114  chr7_KI270807v1_alt         126434    FALSE          HSCHR7_2_CTG7       alt-scaffold  KI270807.1
115  chr7_KI270808v1_alt         271455    FALSE          HSCHR7_3_CTG6       alt-scaffold  KI270808.1
116  chr7_KI270809v1_alt         209586    FALSE        HSCHR7_2_CTG4_4       alt-scaffold  KI270809.1
117  chr7_KI270899v1_alt         190869    FALSE          HSCHR7_2_CTG1       alt-scaffold  KI270899.1
118  chr8_KI270810v1_alt         374415    FALSE          HSCHR8_1_CTG7       alt-scaffold  KI270810.1
119  chr8_KI270811v1_alt         292436    FALSE          HSCHR8_1_CTG1       alt-scaffold  KI270811.1
120  chr8_KI270812v1_alt         282736    FALSE          HSCHR8_2_CTG1       alt-scaffold  KI270812.1
121  chr8_KI270813v1_alt         300230    FALSE          HSCHR8_3_CTG1       alt-scaffold  KI270813.1
122  chr8_KI270814v1_alt         141812    FALSE          HSCHR8_1_CTG6       alt-scaffold  KI270814.1
123  chr8_KI270815v1_alt         132244    FALSE          HSCHR8_2_CTG7       alt-scaffold  KI270815.1
124  chr8_KI270816v1_alt         305841    FALSE          HSCHR8_3_CTG7       alt-scaffold  KI270816.1
125  chr8_KI270817v1_alt         158983    FALSE          HSCHR8_4_CTG7       alt-scaffold  KI270817.1
126  chr8_KI270818v1_alt         145606    FALSE          HSCHR8_4_CTG1       alt-scaffold  KI270818.1
127  chr8_KI270819v1_alt         133535    FALSE          HSCHR8_5_CTG7       alt-scaffold  KI270819.1
128  chr8_KI270820v1_alt          36640    FALSE          HSCHR8_6_CTG7       alt-scaffold  KI270820.1
129  chr8_KI270821v1_alt         985506    FALSE          HSCHR8_8_CTG1       alt-scaffold  KI270821.1
130  chr8_KI270822v1_alt         624492    FALSE          HSCHR8_9_CTG1       alt-scaffold  KI270822.1
131  chr8_KI270900v1_alt         318687    FALSE          HSCHR8_5_CTG1       alt-scaffold  KI270900.1
132  chr8_KI270901v1_alt         136959    FALSE          HSCHR8_6_CTG1       alt-scaffold  KI270901.1
133  chr8_KI270926v1_alt         229282    FALSE          HSCHR8_7_CTG1       alt-scaffold  KI270926.1
134  chr9_GL383539v1_alt         162988    FALSE          HSCHR9_1_CTG1       alt-scaffold  GL383539.1
135  chr9_GL383540v1_alt          71551    FALSE          HSCHR9_1_CTG2       alt-scaffold  GL383540.1
136  chr9_GL383541v1_alt         171286    FALSE          HSCHR9_1_CTG3       alt-scaffold  GL383541.1
137  chr9_GL383542v1_alt          60032    FALSE          HSCHR9_1_CTG4       alt-scaffold  GL383542.1
138  chr9_KI270823v1_alt         439082    FALSE          HSCHR9_1_CTG5       alt-scaffold  KI270823.1
139 chr10_GL383545v1_alt         179254    FALSE         HSCHR10_1_CTG1       alt-scaffold  GL383545.1
140 chr10_GL383546v1_alt         309802    FALSE         HSCHR10_1_CTG2       alt-scaffold  GL383546.1
141 chr10_KI270824v1_alt         181496    FALSE         HSCHR10_1_CTG3       alt-scaffold  KI270824.1
142 chr10_KI270825v1_alt         188315    FALSE         HSCHR10_1_CTG4       alt-scaffold  KI270825.1
143 chr11_GL383547v1_alt         154407    FALSE       HSCHR11_1_CTG1_1       alt-scaffold  GL383547.1
144 chr11_JH159136v1_alt         200998    FALSE HG142_HG150_NOVEL_TEST       alt-scaffold  JH159136.1
145 chr11_JH159137v1_alt         191409    FALSE       HG151_NOVEL_TEST       alt-scaffold  JH159137.1
146 chr11_KI270826v1_alt         186169    FALSE         HSCHR11_1_CTG2       alt-scaffold  KI270826.1
147 chr11_KI270827v1_alt          67707    FALSE         HSCHR11_1_CTG3       alt-scaffold  KI270827.1
148 chr11_KI270829v1_alt         204059    FALSE         HSCHR11_1_CTG5       alt-scaffold  KI270829.1
149 chr11_KI270830v1_alt         177092    FALSE         HSCHR11_1_CTG6       alt-scaffold  KI270830.1
150 chr11_KI270831v1_alt         296895    FALSE         HSCHR11_1_CTG7       alt-scaffold  KI270831.1
151 chr11_KI270832v1_alt         210133    FALSE         HSCHR11_1_CTG8       alt-scaffold  KI270832.1
152 chr11_KI270902v1_alt         106711    FALSE         HSCHR11_2_CTG1       alt-scaffold  KI270902.1
153 chr11_KI270903v1_alt         214625    FALSE       HSCHR11_2_CTG1_1       alt-scaffold  KI270903.1
154 chr11_KI270927v1_alt         218612    FALSE         HSCHR11_3_CTG1       alt-scaffold  KI270927.1
155 chr12_GL383549v1_alt         120804    FALSE         HSCHR12_1_CTG2       alt-scaffold  GL383549.1
156 chr12_GL383550v2_alt         169178    FALSE       HSCHR12_1_CTG2_1       alt-scaffold  GL383550.2
157 chr12_GL383551v1_alt         184319    FALSE       HSCHR12_4_CTG2_1       alt-scaffold  GL383551.1
158 chr12_GL383552v1_alt         138655    FALSE       HSCHR12_2_CTG2_1       alt-scaffold  GL383552.1
159 chr12_GL383553v2_alt         152874    FALSE       HSCHR12_3_CTG2_1       alt-scaffold  GL383553.2
160 chr12_GL877875v1_alt         167313    FALSE         HSCHR12_1_CTG1       alt-scaffold  GL877875.1
161 chr12_GL877876v1_alt         408271    FALSE         HSCHR12_2_CTG2       alt-scaffold  GL877876.1
162 chr12_KI270833v1_alt          76061    FALSE       HSCHR12_5_CTG2_1       alt-scaffold  KI270833.1
163 chr12_KI270834v1_alt         119498    FALSE       HSCHR12_6_CTG2_1       alt-scaffold  KI270834.1
164 chr12_KI270835v1_alt         238139    FALSE         HSCHR12_4_CTG2       alt-scaffold  KI270835.1
165 chr12_KI270836v1_alt          56134    FALSE       HSCHR12_7_CTG2_1       alt-scaffold  KI270836.1
166 chr12_KI270837v1_alt          40090    FALSE         HSCHR12_5_CTG2       alt-scaffold  KI270837.1
 [ reached 'max' / getOption("max.print") -- omitted 289 rows ]

> class(hg_chrs)
[1] "data.frame"

> chr <- subset(hg_chrs[1:24,]) # 一般而言，我们只需要chr1-chr22 & chrX & chrY即可
> chr
   UCSC_seqlevel UCSC_seqlength circular NCBI_seqlevel       SequenceRole GenBankAccn
1           chr1      248956422    FALSE             1 assembled-molecule  CM000663.2
2           chr2      242193529    FALSE             2 assembled-molecule  CM000664.2
3           chr3      198295559    FALSE             3 assembled-molecule  CM000665.2
4           chr4      190214555    FALSE             4 assembled-molecule  CM000666.2
5           chr5      181538259    FALSE             5 assembled-molecule  CM000667.2
6           chr6      170805979    FALSE             6 assembled-molecule  CM000668.2
7           chr7      159345973    FALSE             7 assembled-molecule  CM000669.2
8           chr8      145138636    FALSE             8 assembled-molecule  CM000670.2
9           chr9      138394717    FALSE             9 assembled-molecule  CM000671.2
10         chr10      133797422    FALSE            10 assembled-molecule  CM000672.2
11         chr11      135086622    FALSE            11 assembled-molecule  CM000673.2
12         chr12      133275309    FALSE            12 assembled-molecule  CM000674.2
13         chr13      114364328    FALSE            13 assembled-molecule  CM000675.2
14         chr14      107043718    FALSE            14 assembled-molecule  CM000676.2
15         chr15      101991189    FALSE            15 assembled-molecule  CM000677.2
16         chr16       90338345    FALSE            16 assembled-molecule  CM000678.2
17         chr17       83257441    FALSE            17 assembled-molecule  CM000679.2
18         chr18       80373285    FALSE            18 assembled-molecule  CM000680.2
19         chr19       58617616    FALSE            19 assembled-molecule  CM000681.2
20         chr20       64444167    FALSE            20 assembled-molecule  CM000682.2
21         chr21       46709983    FALSE            21 assembled-molecule  CM000683.2
22         chr22       50818468    FALSE            22 assembled-molecule  CM000684.2
23          chrX      156040895    FALSE             X assembled-molecule  CM000685.2
24          chrY       57227415    FALSE             Y assembled-molecule  CM000686.2

二、获取mouse的染色体信息

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> mm_chrs = fetchExtendedChromInfoFromUCSC('mm10')
> mm_chrs
          UCSC_seqlevel UCSC_seqlength circular      NCBI_seqlevel         SequenceRole GenBankAccn
1                  chr1      195471971    FALSE                  1   assembled-molecule  CM000994.2
2                  chr2      182113224    FALSE                  2   assembled-molecule  CM000995.2
3                  chr3      160039680    FALSE                  3   assembled-molecule  CM000996.2
4                  chr4      156508116    FALSE                  4   assembled-molecule  CM000997.2
5                  chr5      151834684    FALSE                  5   assembled-molecule  CM000998.2
6                  chr6      149736546    FALSE                  6   assembled-molecule  CM000999.2
7                  chr7      145441459    FALSE                  7   assembled-molecule  CM001000.2
8                  chr8      129401213    FALSE                  8   assembled-molecule  CM001001.2
9                  chr9      124595110    FALSE                  9   assembled-molecule  CM001002.2
10                chr10      130694993    FALSE                 10   assembled-molecule  CM001003.2
11                chr11      122082543    FALSE                 11   assembled-molecule  CM001004.2
12                chr12      120129022    FALSE                 12   assembled-molecule  CM001005.2
13                chr13      120421639    FALSE                 13   assembled-molecule  CM001006.2
14                chr14      124902244    FALSE                 14   assembled-molecule  CM001007.2
15                chr15      104043685    FALSE                 15   assembled-molecule  CM001008.2
16                chr16       98207768    FALSE                 16   assembled-molecule  CM001009.2
17                chr17       94987271    FALSE                 17   assembled-molecule  CM001010.2
18                chr18       90702639    FALSE                 18   assembled-molecule  CM001011.2
19                chr19       61431566    FALSE                 19   assembled-molecule  CM001012.2
20                 chrX      171031299    FALSE                  X   assembled-molecule  CM001013.2
21                 chrY       91744698    FALSE                  Y   assembled-molecule  CM001014.2
22                 chrM          16299     TRUE                 MT   assembled-molecule  AY172335.1
23 chr1_GL456210_random         169725    FALSE MMCHR1_RANDOM_CTG1 unlocalized-scaffold  GL456210.1
24 chr1_GL456211_random         241735    FALSE MMCHR1_RANDOM_CTG2 unlocalized-scaffold  GL456211.1
25 chr1_GL456212_random         153618    FALSE MMCHR1_RANDOM_CTG3 unlocalized-scaffold  GL456212.1
26 chr1_GL456213_random          39340    FALSE MMCHR1_RANDOM_CTG4 unlocalized-scaffold  GL456213.1
27 chr1_GL456221_random         206961    FALSE MMCHR1_RANDOM_CTG5 unlocalized-scaffold  GL456221.1
28 chr4_GL456216_random          66673    FALSE      MMCHR4UN_CTG1 unlocalized-scaffold  GL456216.1
29 chr4_GL456350_random         227966    FALSE      MMCHR4UN_CTG3 unlocalized-scaffold  GL456350.1
30 chr4_JH584292_random          14945    FALSE      MMCHR4UN_CTG2 unlocalized-scaffold  JH584292.1
31 chr4_JH584293_random         207968    FALSE      MMCHR4UN_CTG4 unlocalized-scaffold  JH584293.1
32 chr4_JH584294_random         191905    FALSE      MMCHR4UN_CTG5 unlocalized-scaffold  JH584294.1
33 chr4_JH584295_random           1976    FALSE      MMCHR4UN_CTG6 unlocalized-scaffold  JH584295.1
34 chr5_GL456354_random         195993    FALSE MMCHR5_RANDOM_CTG4 unlocalized-scaffold  GL456354.1
35 chr5_JH584296_random         199368    FALSE MMCHR5_RANDOM_CTG1 unlocalized-scaffold  JH584296.1
36 chr5_JH584297_random         205776    FALSE MMCHR5_RANDOM_CTG2 unlocalized-scaffold  JH584297.1
37 chr5_JH584298_random         184189    FALSE MMCHR5_RANDOM_CTG3 unlocalized-scaffold  JH584298.1
38 chr5_JH584299_random         953012    FALSE MMCHR5_RANDOM_CTG5 unlocalized-scaffold  JH584299.1
39 chr7_GL456219_random         175968    FALSE MMCHR7_RANDOM_CTG1 unlocalized-scaffold  GL456219.1
40 chrX_GL456233_random         336933    FALSE MMCHRX_RANDOM_CTG2 unlocalized-scaffold  GL456233.1
41 chrY_JH584300_random         182347    FALSE       MMCHRY_CTGU1 unlocalized-scaffold  JH584300.1
42 chrY_JH584301_random         259875    FALSE       MMCHRY_CTGU2 unlocalized-scaffold  JH584301.1
43 chrY_JH584302_random         155838    FALSE       MMCHRY_CTGU3 unlocalized-scaffold  JH584302.1
44 chrY_JH584303_random         158099    FALSE       MMCHRY_CTGU4 unlocalized-scaffold  JH584303.1
45       chrUn_GL456239          40056    FALSE       MSCHRUN_CTG1    unplaced-scaffold  GL456239.1
46       chrUn_GL456359          22974    FALSE      MSCHRUN_CTG13    unplaced-scaffold  GL456359.1
47       chrUn_GL456360          31704    FALSE      MSCHRUN_CTG14    unplaced-scaffold  GL456360.1
48       chrUn_GL456366          47073    FALSE      MSCHRUN_CTG21    unplaced-scaffold  GL456366.1
49       chrUn_GL456367          42057    FALSE       MSCHRUN_CTG2    unplaced-scaffold  GL456367.1
50       chrUn_GL456368          20208    FALSE      MSCHRUN_CTG22    unplaced-scaffold  GL456368.1
51       chrUn_GL456370          26764    FALSE      MSCHRUN_CTG19    unplaced-scaffold  GL456370.1
52       chrUn_GL456372          28664    FALSE      MSCHRUN_CTG16    unplaced-scaffold  GL456372.1
53       chrUn_GL456378          31602    FALSE       MSCHRUN_CTG3    unplaced-scaffold  GL456378.1
54       chrUn_GL456379          72385    FALSE      MSCHRUN_CTG20    unplaced-scaffold  GL456379.1
55       chrUn_GL456381          25871    FALSE       MSCHRUN_CTG4    unplaced-scaffold  GL456381.1
56       chrUn_GL456382          23158    FALSE       MSCHRUN_CTG5    unplaced-scaffold  GL456382.1
57       chrUn_GL456383          38659    FALSE       MSCHRUN_CTG6    unplaced-scaffold  GL456383.1
58       chrUn_GL456385          35240    FALSE       MSCHRUN_CTG7    unplaced-scaffold  GL456385.1
59       chrUn_GL456387          24685    FALSE      MSCHRUN_CTG17    unplaced-scaffold  GL456387.1
60       chrUn_GL456389          28772    FALSE      MSCHRUN_CTG18    unplaced-scaffold  GL456389.1
61       chrUn_GL456390          24668    FALSE       MSCHRUN_CTG9    unplaced-scaffold  GL456390.1
62       chrUn_GL456392          23629    FALSE      MSCHRUN_CTG10    unplaced-scaffold  GL456392.1
63       chrUn_GL456393          55711    FALSE      MSCHRUN_CTG11    unplaced-scaffold  GL456393.1
64       chrUn_GL456394          24323    FALSE      MSCHRUN_CTG12    unplaced-scaffold  GL456394.1
65       chrUn_GL456396          21240    FALSE      MSCHRUN_CTG15    unplaced-scaffold  GL456396.1
66       chrUn_JH584304         114452    FALSE      MSCHRUN_CTG23    unplaced-scaffold  JH584304.1

> mmchr <- subset(hg_chrs[1:21,])
> mmchr
   UCSC_seqlevel UCSC_seqlength circular NCBI_seqlevel       SequenceRole GenBankAccn
1           chr1      248956422    FALSE             1 assembled-molecule  CM000663.2
2           chr2      242193529    FALSE             2 assembled-molecule  CM000664.2
3           chr3      198295559    FALSE             3 assembled-molecule  CM000665.2
4           chr4      190214555    FALSE             4 assembled-molecule  CM000666.2
5           chr5      181538259    FALSE             5 assembled-molecule  CM000667.2
6           chr6      170805979    FALSE             6 assembled-molecule  CM000668.2
7           chr7      159345973    FALSE             7 assembled-molecule  CM000669.2
8           chr8      145138636    FALSE             8 assembled-molecule  CM000670.2
9           chr9      138394717    FALSE             9 assembled-molecule  CM000671.2
10         chr10      133797422    FALSE            10 assembled-molecule  CM000672.2
11         chr11      135086622    FALSE            11 assembled-molecule  CM000673.2
12         chr12      133275309    FALSE            12 assembled-molecule  CM000674.2
13         chr13      114364328    FALSE            13 assembled-molecule  CM000675.2
14         chr14      107043718    FALSE            14 assembled-molecule  CM000676.2
15         chr15      101991189    FALSE            15 assembled-molecule  CM000677.2
16         chr16       90338345    FALSE            16 assembled-molecule  CM000678.2
17         chr17       83257441    FALSE            17 assembled-molecule  CM000679.2
18         chr18       80373285    FALSE            18 assembled-molecule  CM000680.2
19         chr19       58617616    FALSE            19 assembled-molecule  CM000681.2
20         chr20       64444167    FALSE            20 assembled-molecule  CM000682.2
21         chr21       46709983    FALSE            21 assembled-molecule  CM000683.2
  • 本文作者：括囊无誉
  • 本文链接： CHIPSEQ/chrominfo/
  • 版权声明： 本博客所有文章均为原创作品，转载请注明出处！
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