===== Reading Scaffold from component AGP ===== No errors, no warnings. Objects : 23 - with single component: 13 Scaffolds : 23 - with single component: 13 Components : 95 (W) orientation + : 81 orientation - : 14 orientation ? (formerly 0) : 0 orientation na : 0 Gaps : 72 (N) - do not break scaffold: 72 scaffold, linkage yes: 71 contamination, linkage yes: 1 - break it, linkage no : 0 Linkage evidence: paired-ends : 71 proximity_ligation: 1 Object names : 23 EG1_scaffold[1..23]: 23 Component names : 95 AADB[02037551..02037645].1: 95 #Comment line count : 7 ===== Reading Chromosome from scaffold AGP ===== No errors, no warnings. Objects : 1 - with single component: 0 Scaffolds : 23 - with single component: 23 Components : 23 (W) orientation + : 20 orientation - : 0 orientation ? (formerly 0) : 3 orientation na : 0 Gaps : 24 (N) - do not break scaffold: 0 - break it, linkage no : 24 contig : 21 (100% of N gaps have length=50000) centromere : 1 telomere : 2 (100% of N gaps have length=10000) Most frequent N gap_length (87.5% or 21 lines): 50000 Object names: 1 chrY : 1 Component names : 23 EG1_scaffold[1..23]: 23 #Comment line count : 9 ./test/chr_from_contig_BAC.agp2.0:10:chr37 1 8000000 1 N 8000000 short_arm no na ./test/chr_from_contig_BAC.agp2.0:11:chr37 8000001 8050000 2 N 50000 heterochromatin no na WARNING: two consequtive gap lines (e.g. a gap at the end of a scaffold, two non scaffold-breaking gaps, ...) ./test/chr_from_contig_BAC.agp2.0:12:chr37 8050001 9050000 3 N 1000000 centromere no na WARNING: two consequtive gap lines (e.g. a gap at the end of a scaffold, two non scaffold-breaking gaps, ...) No errors, 2 warnings. Count Code Description 2 w33 two consequtive gap lines (e.g. a gap at the end of a scaffold, two non scaffold-breaking gaps, ...) Objects : 2 - with single component: 0 Scaffolds : 27 - with single component: 13 Components : 208 (W:95, F:80, A:18, D:15) orientation + : 131 orientation - : 77 orientation ? (formerly 0) : 0 orientation na : 0 Gaps : 127 (N:115, U:12) - do not break scaffold: 96 scaffold, linkage yes: 96 - break it, linkage no : 31 contig : 24 (100% of N gaps have length=50000) centromere : 2 (100% of N gaps have length=1000000) short_arm : 1 heterochromatin: 1 telomere : 3 Most frequent N gap_length (21.7% or 25 lines): 50000 Linkage evidence: paired-ends : 79 within_clone: 12 clone_contig: 5 Object names: 2 chrY : 1 chr37 : 1 Component names : 189 AADB[02037551..02037645].1: 95 AC[139190..170923].[1..5] : 94 #Comment line count : 16