Index of /genome/Daphnia_magna/openaccess/genes/Genome/genbank_submit
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dmagna20100422asmfixed.fa.count 25-Jan-2016 19:22 1012k
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Tables on Daphnia magna chromosome assemblies of 454 gdna
Don Gilbert, 2016 Jan
from: genomes@ncbi.nlm.nih.gov
to: gilbertd@indiana.edu
date: Thu, Jan 21, 2016 at 8:46 AM
subject: Accession Daphnia magna Xinb3 (LRGB00000000 ; BioSample SAMN03703141)
We have assigned the following accession number to your submission:
SUBID BioProject BioSample Accession Organism
---------------------------------------------------
SUB1303216 PRJNA298946 SAMN03703141 LRGB00000000 Daphnia magna Xinb3
This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank
under the accession LRGB00000000. The version described in this paper
is version LRGB01000000.
Submission file set
------------------------------------------------------------------------
5.1M Jan 16 16:15 daphmagna_2011pubfc8.aa.gz : proteins of genes
14M Jan 16 16:15 daphmagna_2011pubfc8.gff3.gz : gene annotation in GFF format, from daphmagna_201104m8
2.1M Jan 25 19:38 daphmagna_2011pubfc8.idtab : table of gene ids, public, original, and evg7 hybrid
Dapma1EVg0000000t1, m8AUGnnnn, Dapma7bEVm000000t1
3.3M Jan 16 16:16 daphmagna_2011pubfc8.tbl.gz : annotation tbl format (genbank tbl2asn)
65M Jan 16 16:28 daphmagna_2011pubfc8.gbf.gz : annotation genbank format
269 Jan 16 16:29 daphmagna_2011pubfc8.valsum : tbl2asn val error summary
2.1M Jan 16 14:11 dmagna20100422asmfixed.agp : contig to scaffold AGP table
38M Jan 16 14:13 dmagna20100422asmfixed.fa.gz : chromosome assembly sequence
1012K Jan 25 19:22 dmagna20100422asmfixed.fa.count: chr asm scaffold/contig size table (faCount)
15M Jan 16 14:35 dmagna20100422asmfixed.qual.gz : chr assembly quality scores
868 Jan 13 21:02 dmagna20100422asmfixed.fachanges : changed scaffolds (excluding drops)
Supporting tables
------------------------------------------------------------------------
TABLE A1. Chromosome assemblies of Daphnia magna, 12? chromosomes, of size
estimated at 220 megabases (flow cyto. [ref]), and 227 mb (newbler)
----------------------------------------------------------------------
Chr.assembly Megabases N50 N50s Big AsmMethod DataSource
----------------------------------------------------------------------
a. dmag10 108 64 293k 3.1m Newbler,2010 3209mb/15m 454 reads
b. dmag24nwb7d 118 68 304k 2.8m Newbler,2013 3209mb/15m 454 reads (same as a.)
.. others ..
----------------------------------------------------------------------
Megabases: total chr. assembly size, minus gaps; Big: size of largest chr piece;
N50: count of chr scaffold pieces at 50% base total; N50s: size of scaffold piece at N50;
Daphnia magna chromosome assemblies
dmag10asm : 2010, v2.4, 454 gdna reads, 2010 Newbler version
nwbdmag24g7d : 2015, 454 data of 2010, 2013 Newbler version, -scaffold option
----------------------------------------------------------------------
TABLE A5. Assembly details for dmag10, Newbler v.2.3 (091027_1459)
----------------------------------------------------------------------
Input nReads = 12785963; nPairs= 3151045; nBases = 3209432352; (TABLE A4)
Preasm nReads = 15058514; nBases = 2822113419; after Newbler read processing
Assembled
coverage peakDepth = 13.0; estimatedGenomeSize = 217.0 MB;
nAlignedReads = 8552579 56.8% ; nAlignedBases = 1819200804 64.5%;
nAssembled = 8244025 54.7%; nAssembledBases = 107787551 (-NNN)
nProperPaired = 1423127; nMultiplyMapped = 1048421; nOneMapped = 350651
Unassembled reads (46%):
nRepeats = 5595508 37.2%; nPartial = 304740 2.2%;
nSingletons = 862293 5.7%; nOutlier = 51948 0.4%;
Scaffolds: n=3405; Largest=3718170; N50=545719
All contigs: n=50114; bases=107787551
----------------------------------------------------------------------
from dapmag454gasm/daphmag10geno454NewblerMetrics.txt
TABLE A4. Daphnia magna 454 gDNA read sets, BioProject PRJNA298946, Study SRP064876
---------------------------------------------------------------------------------
Runtype nPair megaBases nReads SRA Accessions and File names
------- ----- --------- ------ -------------------------------------------------
EXPERIMENT reads08 SRX1340073,SRR2664925
SINGLE 0 110.5M 546371 reads.s01r1,reads.s01r2,
SINGLE 0 96.5M 466922 reads.s02r1,reads.s02r2,
SINGLE 0 114.0M 541922 reads.s03r1,reads.s03r2,
SINGLE 0 104.4M 482531 reads.s04r2,reads.s04r1,
SINGLE 0 100.8M 500205 reads.s05r1,reads.s05r2,
SINGLE 0 96.3M 471434 reads.s06r1,reads.s06r2,
EXPERIMENT reads10 SRX1341854,SRR2671171
SINGLE 0 303.8M 1065082 reads.s15r2,reads.s15r1,
SINGLE 0 317.3M 1072889 reads.s16l1r1,reads.s16l1r2,
SINGLE 0 141.6M 590937 reads.s16l3r1,reads.s16l3r2,reads.s16l3r4,
EXPERIMENT pairs08i3k SRX1341948,SRR2671679 insert 2.3kb
PAIRED 209463 127.2M 518690 pairs.s7r2,pairs.s7r1,
PAIRED 168944 108.1M 477436 pairs.s8r1,pairs.s8r2,
PAIRED 195512 118.3M 485444 pairs.s9r1,pairs.s9r2,
PAIRED 200726 122.3M 506555 pairs.s10r2,pairs.s10r1,
PAIRED 222427 133.4M 535542 pairs.s11r2,pairs.s11r1,
PAIRED 217507 131.8M 533032 pairs.s12r2,pairs.s12r1,
PAIRED 245720 149.3M 602317 pairs.s13r1,pairs.s13r2,
EXPERIMENT pairs09i20k SRX1342036,SRR2671858 insert 20kb
PAIRED 268617 158.0M 532372 pairs.s14l1r2,pairs.s14l1r3,pairs.s14l1r1,pairs.s14l1r4,
PAIRED 289298 174.6M 592954 pairs.s14l2r6,pairs.s14l2r5,pairs.s14l2r7,pairs.s14l2r8,
PAIRED 244300 144.4M 548692 pairs.s14l3r1,pairs.s14l3r2,pairs.s14l3r3,pairs.s14l3r4,
PAIRED 255748 135.1M 568084 pairs.s14l4r5,pairs.s14l4r6,pairs.s14l4r7,pairs.s14l4r8,
EXPERIMENT pairs10i8k SRX1341868,SRR2671211 insert 8kb
PAIRED 632783 321.5M 1146552 pairs.s15r1,pairs.s15r2
------ -------- --------- -------------------------------------------------------
Total 3,151,045 3,209M 12,785,963
---------------------------------------------------------------------------------
TABLE A9. Daphnia magna annotated genome submission notes, BioProject PRJNA298946.
---------------------------------------------------------------------------------
version daphmagna_2011pubfc7 (fc7b) ann/asm submitted to ncbi genomes, 2016.01.14
tbl2asn warnings in annotation
2 WARNING: SEQ_FEAT.MultipleGeneOverlap : checked, not cds-overlap but intronic genes
141 WARNING: SEQ_FEAT.ShortExon : checked, mostly high value genes
370 WARNING: SEQ_GRAPH.GraphNScore : qual score>0 but low, Newbler calls N for low-qual bases
10 WARNING: SEQ_FEAT.NotSpliceConsensusAcceptor :
10 WARNING: SEQ_FEAT.NotSpliceConsensusDonor :
462 INFO: SEQ_FEAT.RareSpliceConsensusDonor
ShortExon genes (n=141):
These have been checked and are mostly high value genes (123 orthologs,
133 with expressed transcript equivalents) where tiny exons (some 2,3
bases) were generated by a gene modeller. Though probable artifact
exons, the gene proteins are checked, valid and valuable (published on).
Changes to original chromosome assembly of 2010:
dmagna-v2.4-20100422-assembly contains 40357 entries (3405 scaffolds, 36951 contigs)
- 28956 are submitted as chromosome parts (3404 scaffolds, 25552 contigs)
- 28 entries removed as possible vector or rRNA contaminants (1 scaffold, 27 contigs)
- 11372 tiny contigs removed (size < 200 nt), a few had low qual fragment gene models
- 20 entries were trimmed of NN or vectors (6 scaffolds, 14 contigs), by up to 38 bases.
Changes to original gene set of 2011:
daphmagna_2011 public gene set includes 34614 loci (many annotated as non-coding)
-- 26701 submitted as gene loci, no alternate transcripts
NCBI locus_tag APZ42_000000 corresponding to wfleabase.org GeneID Dapma1EVg000000
-- 14 genes are included as gene fragment misc_feature, due to discrepancies w/ ncbi model
-- 7905 are removed for various reasons:
2481 tiny/fragment, 2950 lowval, 1432 transposon genes,
572 partial-warns, 339 on tiny-scaffolds, 102 overlap-genes,
15 innerstop, 8 contaminant, 4 scaffold-removed
annotations include original id notes "original-id m8AUGepir2s00001g2t1"
annotations include improved hybrid 2014 gene set equivalence "genes-ver7-id Dapma7bEVm030035t1"
Changes v2 (ncbi-fcs):
-- removed 155 tiny contigs flags as contaminant (size 988..202, mostly Thermus thermophilus bacteria)
-- contig fcs-removal took out 55 gene models, all 1-exon, likely fragment, bacterial genes
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