Daphnia pulex Assembly Validation for published JGI JAZZ genome assembly (2007 release) citation = Assembly validation by Jeong-Hyeon Justin Choi, 2007 Analysis types: ARA = Arachne-Jazz validation, PCA = PCAP-Jazz validation, CC= CloneCoverage, RC= ReadCoverage Problem types: compressed, no_match, overlap, partial daphnia_pulex_asmqual.gff.gz The documentation I have is limited. It has locations on the published Dpulex genome assembly 2007 of these Assembly Validation (AV_) features: 92758 AV_ARA 165403 AV_CC 184735 AV_GMB 59825 AV_PCA 163638 AV_RC It is a catenation of these separate analyses, where Validation.GMB = AV_GMB, Validation.CloneCoverage = AV_CC, Validation.ReadCoverage = AV_RC Arachne-Jazz validation = AV_ARA, PCAP-Jazz validation = AV_PCA === arachne-jazz.mummer.filter100.spr.br.scaffold.gff.gz === ##gff-version 3 # analysis-source: AV_ARA = Arachne-Jazz validation (Mummer) #ref source type start end score scaffold_1 AV_ARA region 1 4 0 . . ID=AV_ARA_1;type=no_match;Target=contig_16661 1 4 scaffold_1 AV_ARA region 563 2011 0 . . ID=AV_ARA_2;type=overlap;Target=contig_16661 563 2011 scaffold_1 AV_ARA region 2295 2353 0 . . ID=AV_ARA_3;type=overlap;Target=contig_16661 2295 2353 scaffold_1 AV_ARA region 3056 3743 0 . . ID=AV_ARA_4;type=overlap;Target=contig_16661 3056 3743 scaffold_1 AV_ARA region 3766 4770 0 . . ID=AV_ARA_5;type=overlap;Target=contig_16661 3766 4770 scaffold_1 AV_ARA region 5885 6003 1 . . ID=AV_ARA_6;type=no_match;Target=contig_25572 1 119 scaffold_1 AV_ARA region 6003 6003 1 . . ID=AV_ARA_7;Parent=AV_ARA_6;type=partial;Target=contig_25572 119 119 === contigs.clone.cover.gmb.scaffold.gff.gz === ##gff-version 3 #ref source type start end score scaffold_1 Validation GMB 1 167 -1 . . ID=AV_GMB_000000001;region=contig_16661:1-167 scaffold_1 Validation GMB 168 182 -2 . . ID=AV_GMB_000000002;region=contig_16661:168-182 scaffold_1 Validation GMB 183 230 -3 . . ID=AV_GMB_000000003;region=contig_16661:183-230 scaffold_1 Validation GMB 231 314 -4 . . ID=AV_GMB_000000004;region=contig_16661:231-314 scaffold_1 Validation GMB 315 387 -5 . . ID=AV_GMB_000000005;region=contig_16661:315-387 scaffold_1 Validation GMB 388 487 -6 . . ID=AV_GMB_000000006;region=contig_16661:388-487 scaffold_1 Validation GMB 488 587 -7 . . ID=AV_GMB_000000007;region=contig_16661:488-587 scaffold_1 Validation GMB 588 621 -8 . . ID=AV_GMB_000000008;region=contig_16661:588-621 === contigs.clone.cover.lander.scaffold.gff.gz === ##gff-version 3 #ref source type start end score scaffold_1 Validation CloneCoverage 1 167 2.077e-10 . . ID=AV_CC_000000001;Coverage=1;region=contig_16661:1-167 scaffold_1 Validation CloneCoverage 168 182 2.652e-09 . . ID=AV_CC_000000002;Coverage=2;region=contig_16661:168-182 scaffold_1 Validation CloneCoverage 7147 7244 2.652e-09 . . ID=AV_CC_000000003;Coverage=2;region=contig_25572:1263-1360 scaffold_1 Validation CloneCoverage 7245 7453 2.077e-10 . . ID=AV_CC_000000004;Coverage=1;region=contig_25572:1361-1569 scaffold_1 Validation CloneCoverage 24792 25119 2.077e-10 . . ID=AV_CC_000000005;Coverage=1;region=contig_15108:1-328 scaffold_1 Validation CloneCoverage 25120 25198 2.652e-09 . . ID=AV_CC_000000006;Coverage=2;region=contig_15108:329-407 scaffold_1 Validation CloneCoverage 25559 25699 2.652e-09 . . ID=AV_CC_000000007;Coverage=2;region=contig_15108:768-908 scaffold_1 Validation CloneCoverage 131173 131179 2.652e-09 . . ID=AV_CC_000000008;Coverage=2;region=contig_42399:894-900 === contigs.read.cover.lander.scaffold.gff.gz === ##gff-version 3 #ref source type start end score scaffold_1 Validation ReadCoverage 1 167 0.01047 . . ID=AV_RC_000000001;Coverage=1;region=contig_16661:1-167 scaffold_1 Validation ReadCoverage 3317 3596 0.01047 . . ID=AV_RC_000000002;Coverage=1;region=contig_16661:3317-3596 scaffold_1 Validation ReadCoverage 3715 3849 0.01047 . . ID=AV_RC_000000003;Coverage=1;region=contig_16661:3715-3849 scaffold_1 Validation ReadCoverage 4840 4931 0.01047 . . ID=AV_RC_000000004;Coverage=1;region=contig_16661:4840-4931 scaffold_1 Validation ReadCoverage 5885 5996 0.01047 . . ID=AV_RC_000000005;Coverage=1;region=contig_25572:1-112 scaffold_1 Validation ReadCoverage 7245 7453 0.01047 . . ID=AV_RC_000000006;Coverage=1;region=contig_25572:1361-1569 scaffold_1 Validation ReadCoverage 24792 25119 0.01047 . . ID=AV_RC_000000007;Coverage=1;region=contig_15108:1-328 scaffold_1 Validation ReadCoverage 25598 25699 0.01047 . . ID=AV_RC_000000008;Coverage=1;region=contig_15108:807-908 === pcap-jazz.mummer.filter100.spr.br.scaffold.gff.gz === ##gff-version 3 # analysis-source: AV_PCA = PCAP-Jazz validation (Mummer) #ref source type start end score scaffold_1 AV_PCA region 212 4005 1 . . ID=AV_PCA_1;type=overlap;Target=contig_16661 212 4005 scaffold_1 AV_PCA region 1760 1760 1 . . ID=AV_PCA_2;Parent=AV_PCA_1;type=compressed;Target=contig_16661 1760 1760 scaffold_1 AV_PCA region 4879 4921 1 . . ID=AV_PCA_3;type=no_match;Target=contig_16661 4879 4921 scaffold_1 AV_PCA region 4879 4879 1 . . ID=AV_PCA_4;Parent=AV_PCA_3;type=partial;Target=contig_16661 4879 4879 scaffold_1 AV_PCA region 5885 5885 0 . . ID=AV_PCA_5;type=no_match;Target=contig_25572 1 1 scaffold_1 AV_PCA region 6004 6824 2 . . ID=AV_PCA_6;type=overlap;Target=contig_25572 120 940 scaffold_1 AV_PCA region 6004 6004 1 . . ID=AV_PCA_7;Parent=AV_PCA_6;type=compressed;Target=contig_25572 120 120