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NA12878_prelim_3.0

Description:
MGI Reference Genomes Project NA12878 preliminary assembly version 3
Organism name:
Homo sapiens (human)
Isolate:
NA12878
Sex:
female
BioSample:
SAMN05181962
BioProject:
PRJNA323611
Submitter:
The Genome Institute at Washington University School of Medicine
Date:
2018/02/09
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_002077035.3 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
NBMU01
Assembly method:
Falcon v. November 2016
Expected final version:
no
Genome coverage:
75x
Sequencing technology:
PacBio RSII

IDs: 1559891 [UID] 6011548 [GenBank]

See Genome Information for Homo sapiens

There are 1044 assemblies for this organism

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History (Show revision history)

Comment

This chromosome-level assembly of the NA12878 genome, NA12878_prelim_3.0, is a draft and represents a work in progress. It will subsequently be re-submitted with BACs incorporated into regions of the genome that are difficult to assemble. Also, single allelic representations ... of specific regions will be added when available.
Sequence Assembly Release Notes for Homo sapiens NA12878_prelim_3.0
 Background:
 DNA used for shotgun sequencing is derived from the blood, b-lymphocytes cells, of an adult female, identified as NA12878 (Coriell Institute for Medical Research). The NA12878 genome is diploid and from a CEPH/UTAH pedigree 1463. Sequence from this project will be used to improve the contiguity of the human reference sequence and add diverse allelic variation.
 Total sequence (subreads) input coverage on the PacBio RS II instrument was 70x prior to error correction using a genome size estimate of 3Gb. The combined sequence reads were assembled using the Falcon software, and then error corrected using the Quiver and Pilon algorithms. Contigs of 200 bp or less have been excluded from NA12878_prelim_3.0.
 This work was supported by the NHGRI 'Improving The Human Reference Genome Resource' grant no. 5U41HG007635 to Richard K. Wilson, at the McDonnell Genome Institute, Washington University School of Medicine.
 DNA Source Contact: Dr. Fedik Rahimov, at the Coriell Institute for Medical Research.

24 contigs have been split and replaced by 52 new contigs, so there are only 3663 live contigs.  more

Global statistics

Total sequence length3,088,210,890
Total ungapped length2,851,295,621
Gaps between scaffolds179
Number of scaffolds2,221
Scaffold N5089,003,101
Scaffold L5014
Number of contigs3,220
Contig N5016,821,028
Contig L5054
Total number of chromosomes and plasmids23
Number of component sequences (WGS or clone)3,663

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
Assembly Unit: Primary Assembly (GCA_002077115.3)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM009447.1n/an/a0
Chromosome 2CM009448.1n/an/a0
Chromosome 3CM009449.1n/an/a0
Chromosome 4CM009450.1n/an/a0
Chromosome 5CM009451.1n/an/a0
Chromosome 6CM009452.1n/an/a0
Chromosome 7CM009453.1n/an/a0
Chromosome 8CM009454.1n/an/a0
Chromosome 9CM009455.1n/an/a0
Chromosome 10CM009456.1n/an/a0
Chromosome 11CM009457.1n/an/a0
Chromosome 12CM009458.1n/an/a0
Chromosome 13CM009459.1n/an/a0
Chromosome 14CM009460.1n/an/a0
Chromosome 15CM009461.1n/an/a0
Chromosome 16CM009462.1n/an/a0
Chromosome 17CM009463.1n/an/a0
Chromosome 18CM009464.1n/an/a0
Chromosome 19CM009465.1n/an/a0
Chromosome 20CM009466.1n/an/a0
Chromosome 21CM009467.1n/an/a0
Chromosome 22CM009468.1n/an/a0
Chromosome XCM009469.1n/an/a0
unplacedn/an/an/a2,119

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All3,088,210,8902,2212,851,295,62189,003,101999179
Chromosome 1249,280,7354220,893,639121,675,614948
Chromosome 2242,066,3735234,876,485147,472,534808
Chromosome 3198,341,3133194,640,468104,467,127235
Chromosome 4189,794,4543185,748,895138,065,967354
Chromosome 5181,895,2612175,220,040131,329,590335
Chromosome 6170,742,3852167,712,320110,228,390235
Chromosome 7160,125,0644152,478,51797,183,854826
Chromosome 8145,194,7875141,572,51939,726,706268
Chromosome 9138,577,51113112,266,85269,997,0876717
Chromosome 10134,061,6872129,473,06892,102,678433
Chromosome 11135,429,8142129,462,02880,181,292267
Chromosome 12133,317,3712130,206,54196,115,952234
Chromosome 13114,461,236295,660,48795,916,644118
Chromosome 14106,626,693187,516,11288,293,070236
Chromosome 15102,313,910179,453,55482,495,101495
Chromosome 1690,760,118576,449,70843,815,780679
Chromosome 1783,164,095576,736,47456,151,880627
Chromosome 1880,465,171274,430,78559,382,565174
Chromosome 1959,280,631254,161,42631,812,276847
Chromosome 2064,912,682760,691,73233,154,8312310
Chromosome 2147,467,6211335,326,94033,776,8522518
Chromosome 2251,550,5101535,027,40932,219,7244320
Chromosome X155,131,0452148,039,19993,059,013405
unplaced53,250,4232,11953,250,42336,45200
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