1000genomes Reference Genome Sequence (hs37d5)

Description

Full 1000genomes Phase2 Reference Genome Sequence (hs37d5), based on NCBI GRCh37.

Note

This BSgenome data package was made from the following source data file:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz

The genome is composed of:

• Integrated reference sequence from the GRCh37 primary assembly (chromosomal plus unlocalized and unplaced contigs)

• The rCRS mitochondrial sequence (AC:NC_012920)

• Human herpesvirus 4 type 1 (AC:NC_007605)

• Concatenated decoy sequences (hs37d5cs.fa.gz)

For details, please see ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/README_human_reference_20110707.

Author(s)

Julian Gehring <julian.gehring@embl.de>

See Also

• BSgenome objects and the available.genomes function in the BSgenome software package.

• DNAString objects in the Biostrings package.

• The BSgenomeForge vignette (vignette("BSgenomeForge")) in the BSgenome software package for how to make a BSgenome data package.

Examples

BSgenome.Hsapiens.1000genomes.hs37d5
genome <- BSgenome.Hsapiens.1000genomes.hs37d5
seqlengths(genome)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(BSgenome.Hsapiens.1000genomes.hs37d5)
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/BSgenome.Hsapiens.1000genomes.hs37d5/package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BSgenome.Hsapiens.1000genomes.hs37d5
> ### Title: 1000genomes Reference Genome Sequence (hs37d5)
> ### Aliases: BSgenome.Hsapiens.1000genomes.hs37d5-package
> ###   BSgenome.Hsapiens.1000genomes.hs37d5 hs37d5
> ### Keywords: package data
> 
> ### ** Examples
> 
> BSgenome.Hsapiens.1000genomes.hs37d5
Human genome:
# organism: Homo sapiens (Human)
# provider: 1000genomes
# provider version: hs37d5
# release date: 2011-07-07
# release name: hs37d5
# 86 sequences:
#   1          2          3          4          5          6          7         
#   8          9          10         11         12         13         14        
#   15         16         17         18         19         20         21        
#   22         X          Y          MT         GL000207.1 GL000226.1 GL000229.1
#   GL000231.1 GL000210.1 GL000239.1 GL000235.1 GL000201.1 GL000247.1 GL000245.1
#   ...        ...        ...        ...        ...        ...        ...       
#   GL000198.1 GL000208.1 GL000191.1 GL000227.1 GL000228.1 GL000214.1 GL000221.1
#   GL000209.1 GL000218.1 GL000220.1 GL000213.1 GL000211.1 GL000199.1 GL000217.1
#   GL000216.1 GL000215.1 GL000205.1 GL000219.1 GL000224.1 GL000223.1 GL000195.1
#   GL000212.1 GL000222.1 GL000200.1 GL000193.1 GL000194.1 GL000225.1 GL000192.1
#   NC_007605  hs37d5                                                           
# (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
# to access a given sequence)
> genome <- BSgenome.Hsapiens.1000genomes.hs37d5
> seqlengths(genome)
         1          2          3          4          5          6          7 
 249250621  243199373  198022430  191154276  180915260  171115067  159138663 
         8          9         10         11         12         13         14 
 146364022  141213431  135534747  135006516  133851895  115169878  107349540 
        15         16         17         18         19         20         21 
 102531392   90354753   81195210   78077248   59128983   63025520   48129895 
        22          X          Y         MT GL000207.1 GL000226.1 GL000229.1 
  51304566  155270560   59373566      16569       4262      15008      19913 
GL000231.1 GL000210.1 GL000239.1 GL000235.1 GL000201.1 GL000247.1 GL000245.1 
     27386      27682      33824      34474      36148      36422      36651 
GL000197.1 GL000203.1 GL000246.1 GL000249.1 GL000196.1 GL000248.1 GL000244.1 
     37175      37498      38154      38502      38914      39786      39929 
GL000238.1 GL000202.1 GL000234.1 GL000232.1 GL000206.1 GL000240.1 GL000236.1 
     39939      40103      40531      40652      41001      41933      41934 
GL000241.1 GL000243.1 GL000242.1 GL000230.1 GL000237.1 GL000233.1 GL000204.1 
     42152      43341      43523      43691      45867      45941      81310 
GL000198.1 GL000208.1 GL000191.1 GL000227.1 GL000228.1 GL000214.1 GL000221.1 
     90085      92689     106433     128374     129120     137718     155397 
GL000209.1 GL000218.1 GL000220.1 GL000213.1 GL000211.1 GL000199.1 GL000217.1 
    159169     161147     161802     164239     166566     169874     172149 
GL000216.1 GL000215.1 GL000205.1 GL000219.1 GL000224.1 GL000223.1 GL000195.1 
    172294     172545     174588     179198     179693     180455     182896 
GL000212.1 GL000222.1 GL000200.1 GL000193.1 GL000194.1 GL000225.1 GL000192.1 
    186858     186861     187035     189789     191469     211173     547496 
 NC_007605     hs37d5 
    171823   35477943 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>