BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068131.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,583,262 number of mapped reads = 3,394,430 (94.73%) number of supplementary alignments = 16,778 (0.47%) number of secondary alignments = 0 number of mapped bases = 219,875,649 bp number of sequenced bases = 219,791,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,338,952 duplication rate = 18.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9758 >>>>>>> ACTG content number of A's = 58,627,280 bp (26.67%) number of C's = 39,150,885 bp (17.81%) number of T's = 72,044,397 bp (32.78%) number of G's = 49,944,130 bp (22.72%) number of N's = 24,819 bp (0.01%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,109,320 number of insertions = 14,273 mapped reads with insertion percentage = 0.42% number of deletions = 47,497 mapped reads with deletion percentage = 1.38% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.071X std coverageData = 0.9255X There is a 1.63% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 16660621 0.06684284650187491 1.2110929037653086 chr2 243199373 16629239 0.06837698138308934 0.99199645639265 chr3 198022430 16760909 0.08464146713076898 0.8473891388716404 chr4 191154276 14978765 0.07835956021198291 0.8450078534444968 chr5 180915260 8926498 0.049340768711274 0.6595975274626911 chr6 171115067 15987373 0.0934305393457842 0.906644798067691 chr7 159138663 21612961 0.13581213133605377 1.2203026988671009 chr8 146364022 7944275 0.05427751227005773 1.3102611154634018 chr9 141213431 10513327 0.07444990838017383 0.8254015530517889 chr10 135534747 11883795 0.08768079966977028 1.12821554143292 chr11 135006516 10028969 0.07428507376636546 0.8560687023664911 chr12 133851895 6823848 0.050980585668958966 0.6699951378739166 chr13 115169878 4720969 0.040991351922765776 0.6074602034458664 chr14 107349540 8146471 0.07588733961971332 0.8059686879493788 chr15 102531392 5454308 0.05319646884341529 0.6597138227666874 chr16 90354753 4197480 0.04645555281413918 0.645855864051599 chr17 81195210 5426470 0.06683239072846785 0.7845280666273446 chr18 78077248 5804994 0.07434936743672113 1.0665984466637812 chr19 59128983 3623722 0.06128503850641233 0.9090989780366989 chr20 63025520 3294976 0.052280028788338435 0.6748041640190758 chr21 48129895 4170733 0.08665576768866834 0.8653894518195825 chr22 51304566 869711 0.01695192197903009 0.3967566842743425 chrMT 16571 465689 28.102649206444994 31.421979031306247 chrX 155270560 14303127 0.09211744325517986 0.9564962665527527 chrY 59373566 646419 0.01088731978806865 0.26706329899172665