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HG00514_prelim_3.0

Organism name:
Homo sapiens (human)
Isolate:
HG00514
Sex:
female
BioSample:
SAMN04229552
BioProject:
PRJNA300843
Submitter:
The Genome Institute at Washington University School of Medicine
Date:
2018/05/22
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_002180035.3 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
NIOH01
Assembly method:
Falcon v. November 2016
Expected final version:
no
Genome coverage:
80.0x
Sequencing technology:
PacBio RSII

IDs: 1716181 [UID] 6535938 [GenBank]

See Genome Information for Homo sapiens

There are 1082 assemblies for this organism

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History (Show revision history)

Comment


Sequence Assembly Release Notes - Homo sapiens HG00514_prelim_3.0

 This is a chromosome-level assembly of the HG00514 genome. HG00514_prelim_3.0 is a draft and represents a work in progress. It will subsequently be re-submitted with additional scaffold and/or chromosome structure. These ... updates are expected within a few months of the initial submission date.

 Background:

 The HG00514 DNA for shotgun sequencing is derived from the blood, b-lymphocytes cells, of an adult female from the Coriell Institute for Medical Research. The HG00514 genome is diploid and from a Southern Han Chinese pedigree SH032. 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 79.9X 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. This HG00514_prelim_3.0 version has been cleaned, and contigs 200bp and less were removed. The assembly is made up of contigs with an N50 contig length of 25.3Mb. The assembly spans 2.87Gb.

 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

 In the previous version, HG00514_prelim_2.1, 29 contigs were split and replaced by 59 new contigs. The suppressed contigs are NIOH01000006.1, NIOH01000022.1, NIOH01000133.1, NIOH01000203.1, NIOH01000242.1, NIOH01000248.1, NIOH01000279.1, NIOH01000282.1, NIOH01000283.1, NIOH01000292.1, NIOH01000319.1, NIOH01000338.1, NIOH01000358.1, NIOH01000365.1, NIOH01000412.1, NIOH01000415.1, NIOH01000422.1, NIOH01000451.1, NIOH01000514.1, NIOH01000601.1, NIOH01000609.1, NIOH01000611.1, NIOH01000631.1, NIOH01000665.1, NIOH01000681.1, NIOH01000782.1, NIOH01000821.1, NIOH01001018.1, NIOH01001196.1. The new contigs are NIOH01003161-NIOH01003219.  more

Global statistics

Total sequence length3,094,330,096
Total ungapped length2,864,989,099
Gaps between scaffolds161
Number of scaffolds2,226
Scaffold N5089,384,495
Scaffold L5014
Number of contigs2,877
Contig N5029,396,877
Contig L5031
Total number of chromosomes and plasmids23
Number of component sequences (WGS or clone)3,190

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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_002180045.3)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM009872.1n/an/a0
Chromosome 2CM009873.1n/an/a0
Chromosome 3CM009874.1n/an/a0
Chromosome 4CM009875.1n/an/a0
Chromosome 5CM009876.1n/an/a0
Chromosome 6CM009877.1n/an/a0
Chromosome 7CM009878.1n/an/a0
Chromosome 8CM009879.1n/an/a0
Chromosome 9CM009880.1n/an/a0
Chromosome 10CM009881.1n/an/a0
Chromosome 11CM009882.1n/an/a0
Chromosome 12CM009883.1n/an/a0
Chromosome 13CM009884.1n/an/a0
Chromosome 14CM009885.1n/an/a0
Chromosome 15CM009886.1n/an/a0
Chromosome 16CM009887.1n/an/a0
Chromosome 17CM009888.1n/an/a0
Chromosome 18CM009889.1n/an/a0
Chromosome 19CM009890.1n/an/a0
Chromosome 20CM009891.1n/an/a0
Chromosome 21CM009892.1n/an/a0
Chromosome 22CM009893.1n/an/a0
Chromosome XCM009894.1n/an/a0
unplacedn/an/an/a2,128

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All3,094,330,0962,2262,864,989,09989,384,495651161
Chromosome 1249,025,2585221,252,994121,337,274576
Chromosome 2242,108,5325235,298,153147,572,243637
Chromosome 3198,656,2453195,197,835104,621,282185
Chromosome 4189,902,3133186,110,683138,153,782214
Chromosome 5182,359,0742175,795,056131,928,221375
Chromosome 6170,773,6302167,965,731110,643,105165
Chromosome 7160,172,9844153,423,38897,239,487605
Chromosome 8145,597,5365141,619,45839,708,623138
Chromosome 9138,185,08516111,465,50969,984,1563819
Chromosome 10134,284,7202129,528,62692,325,635283
Chromosome 11134,986,0432130,068,74280,619,734187
Chromosome 12133,424,5073130,497,56095,045,573124
Chromosome 13114,326,849295,833,89995,849,75477
Chromosome 14106,462,050187,368,54687,964,384145
Chromosome 15103,131,112179,835,84083,345,558505
Chromosome 1690,548,316477,127,91143,791,677497
Chromosome 1783,312,180377,246,31456,231,447356
Chromosome 1880,431,957274,370,36959,408,55195
Chromosome 1958,861,501255,383,83331,414,415156
Chromosome 2064,569,730559,953,46833,196,184108
Chromosome 2147,243,6501335,437,77833,822,4342317
Chromosome 2251,405,0371135,041,28232,204,8012614
Chromosome X155,249,3552149,853,69293,294,898323
unplaced59,312,4322,12859,312,43243,60400
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