Tables on Daphnia magna chromosome assemblies of 454 gdna Don Gilbert, 2016 Jan TABLE A1. Chromosome assemblies of Daphnia magna TABLE A2. Gene mappings to chromosome assemblies TABLE A3. Unassembled 454 gDNA genic/intergenic alignments, showing genic excess TABLE A4. Daphnia magna 454 gDNA read sets, BioProject PRJNA298946 TABLE A5. Assembly details for dmag10, Newbler v.2.3 (091027_1459) TABLE A6. Assembly details for nwbdmag24g7d, Newbler v.2.9 (20130529_1641) ---------------------------------------------------------------------- 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 b2. dmag24nwb7dla2 118 13 1317k 17m (b)+EvigeneScaf (b)+ 4720 split-gene blastn mappings b3. dmag24nwb7dla3 118 4 10962k 19m (b)+EvigeneScaf (b)+ 5230 split-gene splign mappings c. dmag14bgi2 210 180 207k 6.2m SOAP,2014 ??? mb Illumina reads c' dmag14bgi2 -- 41 788k 6.2m (c) adjust for same size as (a,b) ---------------------------------------------------------------------- Megabases: total chr. assembly size, minus gaps; Big: size of largest chr piece; N50: count of chr pieces at 50% base total; N50s: size of scaffold 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 dmag24nwb7dla2: 2015, same contigs as nwbdmag24g7d, re-scaffold with gene-blastn + evg-lachesis dmag24nwb7dla3: 2015, same contigs as nwbdmag24g7d, re-scaffold with gene-splign + evg-lachesis dmag14bgi2 : 2014, Illumina gdna assembly, BGI v2 ---------------------------------------------------------------------- TABLE A2. Gene mappings to chromosome assemblies -------------------------------------------------------------------- Chr_assembly Gene locus mapping counts nSingle nDuplicate nMapped noMap nSplit* -------------------------------------------------------------------- a. dmag10asm 25729 434 (205) 26163 3200 5399 b. dmag24nwb7d 25856 602 (285) 26458 2993 3366 b2. dmag24nwb7dla2 26009 602 (287) 26611 2838 2168 b3. dmag24nwb7dla3 26110 616 (291) 26726 2733 2168 c. dmag14bgi2 25312 3115 (1288) 28427 2534 4156 UnionOfAbove 25132 3810 (1611) 28942 2391 -- -------------------------------------------------------------------- nSingle = one Chr_assembly location/gene (counting splits as 1 location) nDuplicate= multiple Chr_assembly locations/gene, with ndup locations (ngene ids) nMapped = total of nSingle + nDuplicate mappable loci noMap = no Chr_assembly location/gene nSplit = genes split over scaffolds, need to check recount * Gene set is dmag7finall9b (Dapma7bEVm000000) with 29134 gene assemblies or loci (of distinct exon sets), and 114009 transcripts, where best mapped transcript/locus is counted for stats gene x chr mapping method: gmap, 2014 version ---------------------------------------------------------------------- TABLE A3. Unassembled 454 gDNA genic/intergenic alignments, showing unassembled excess in genic spans, for dmag24nwb7d assembly (TABLE A6) ---------------------------------------------------------------------- Query_ID Hit% Align% Ident% nHit bMatch bFull -------------------------------------------------------------------- Unassembled Repeats (21%, n=2623901) mRNA transcripts 70.4 37.8 99.8 1848511 155848091 92840498 intergenic 54.1 17.1 99.8 1419949 55015587 2656732 Unassembled Singles (11%, n=1225099) mRNA transcripts 58.1 53.6 99.9 712304 44783349 2232053 intergenic 42.9 44.1 99.9 525582 27939845 598868 Assembled read subset (64%, sample n=896384) mRNA transcripts 52.7 68.7 99.8 472624 71960431 134820754 intergenic 46.0 71.7 99.8 412127 65124518 40026841 -------------------------------------------------------------------- blat align of gdna Unassembled/Assembled read subsets, using reads >= 70nt mRNA transcripts: pubevg/dmagset7pub9dup.mrna, bases=47,635,479 intergenic : nwbdmag24g7d_intergene.fa, bases=45,150,786 (excluding gaps, ie about same size as mrna) (intergenic chromosome assembly is sequence of nwbdmag24g7d outside of gene exons, summing parts>100bp) Hit%: reads align >= 25%, and nHit, of input read sets; Align%: aligned portion of hit reads total length; Ident%: bases match/(match+mismatch) percent bMatch: bases of >= 25% align; bFull: bases of >= 90% align of read ----------------------------------------------------------------------------------- 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 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 A6. Assembly details for nwbdmag24g7d, Newbler v.2.9 (20130529_1641) ---------------------------------------------------------------------- Input nReads = 12785963; nPairs= 3151045; nBases = 3209432352; (TABLE A4) Preasm nReads = 15707284; nBases = 2947678588; after Newbler read processing Assembled Coverage peakDepth = 13.0; estimatedGenomeSize = 227.0 MB; nAlignedReads = 10593243 67.44% ; nAlignedBases = 2162983966 73.38%; nAssembled = 10029045 63.85%; nAssembledBases = 117483510 (-NNN) nProperPaired = 2016202; nMultiplyMapped = 774430; nOneMapped = 301099 Unassembled reads (36%): nRepeats = 3332814 21.2%; nPartial = 562419 3.6%; nSingletons = 1736006 11.0%; nOutlier = 47000 0.3%; Scaffolds: n=2234; Largest=3111085; N50=564772 All contigs: n=72358; bases=119215380 ---------------------------------------------------------------------- from dapmag454gasm/daphmag24i7c454NewblerMetrics.txt