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Chrysemys_picta_bellii-3.0.1

Organism name:
Chrysemys picta bellii (western painted turtle)
Isolate:
RCT428
Sex:
female
Submitter:
Painted turtle genome sequencing consortium
Date:
2012/01/09
Synonyms:
chrPic1
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_000241765.1 (replaced)
RefSeq assembly accession:
GCF_000241765.2 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: 4 unlocalized scaffolds on chromosome MT.
  • Only in RefSeq: chromosome MT.
  • Data displayed for RefSeq version
WGS Project:
AHGY01
Assembly method:
Newbler v. 2.6
Genome coverage:
15x
Sequencing technology:
Sanger; 454

IDs: 49541 [UID] 326468 [GenBank] 753318 [RefSeq]

See Genome Information for Chrysemys picta

History (Show revision history)

Comment

The Chrysemys picta bellii, the painted turtle, whole genome shotgun library from primary donor-derived reads (Field number: RCT428 Locality: WA: Grant Co: small lake 1.3 miles south of Potholes Reservoir) were assembled using Newbler (version 2.6) using stringent parameters. ... The resulting assembly was labeled as 3.0.1. After the assembly was complete, 15X of paired end sequencing data were generated on the Illumina platform and used for error correction in the reference assembly (see below). All scaffolds larger than 500 bases (81,642 scaffolds with a total size of 2618Mb, N50 scaffold size of 3.01Mb (N50 number is 248)) were retained for submission to the public databases.
For error correction, the Illumina data were aligned against the 3.0.1 assembly using bwa and processed using samtools and bcftools. Based on the paired end mapping data, all duplicately mapped reads were removed. One and two basepair indels were introduced into the reference for all cases where there were >=3 and <200 reads aligned (mapping quality >=40 and the indel was >=10 bases from the end of the alignment), and where all reads disagreed with the reference and agreed with one another. There were a total of 27,296 indels introduced into 24,712 contigs.
The assembly data were aligned at UCSC (B. Raney) utilizing BLASTZ (Schwartz 2003) to align and score non-repetitive turtle regions against the following repeat-masked genomes: lizard (anoCar2), human (hg19), chicken (galGal3) and opossum (monDom5). Alignment chains differentiated between orthologous and paralogous alignments (Kent 2003) and only "reciprocal best" alignments were retained in the alignment set. The alignments were post-filtered in the following ways: (1) only alignments that extended over at least 2000 bases where the relative expansion/contraction was less than 10X were retained, (2) alignments were then smoothed by removing any single alignments that were <10kb and occurred as a single alignment in between a large block of separate alignments to the same chromosome. The relative scaffold ordering was then examined in the four pairwise alignments. If at least three of the different pairwise alignments with the other species all suggested a given order and orientation, that pairwise ordered was retained in a list of valid orders (and orientations). Then the consistent pairwise alignments were linked into groups. The AGP was created by using those lists of ordered and oriented scaffolds. Because ordering by homology is not absolutely confident, the gaps between scaffolds were annotated with linkage evidence align_xgenus in the AGP file, format 2.0. There was approximately 1Gb of sequence organized into ordered groups.

Background information on the Chrysemys picta bellii genome sequencing project and the initial news release about the Chrysemys picta bellii assembly can be found on the Washington University School of Medicine website.
Bulk downloads of the sequence and annotation data are available via GenBank, Ensembl, DDBJ and the UCSC Genome Browser. The complete set of sequence reads is available at the NCBI Trace archive.

Credits: Genome Sequence - Washington University School of Medicine Sequence Assembly and Chromosomal Sequence/AGP Construction - Washington University School of Medicine
DNA sources: WGS library; UC-Davis Shaffer lab; Female; Chrysemys picta bellii ; Field number: RCT428 (This will later have an MVZ number assigned) ; Locality: WA: Grant Co: small lake 1.3 miles south of Potholes Reservoir BAC Library VMRC CHY3; J. Froula JGI (from C. Amemiya Lab) Female; Strain MVZ #238119; Locality: WA: Grant Co: small lake 1.3 miles south of Potholes Reservoir
Read Types: 11.3X 454 fragments 6.5X 454 3 Kb inserts 1.3X 454 8 Kb inserts 0.06X Sanger BAC-end sequences
Funding for the sequence characterization of the Chrysemys picta bellii genome is being provided by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).  more

Global statistics

Total sequence length2,589,745,704
Total assembly gap length431,452,339
Gaps between scaffolds0
Number of scaffolds80,984
Scaffold N505,212,367
Scaffold L50148
Number of contigs551,713
Contig N5011,852
Contig L5045,209
Total number of chromosomes and plasmids1

Supplemental Content

PubMed articles for this assembly

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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
non-nuclear
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced2,589,728,83880,9832,158,276,4995,212,367470,7290
MoleculeTotal
Length
Mitochondrion MT16,866
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