BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054620.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 13,232,344 number of mapped reads = 10,661,002 (80.57%) number of supplementary alignments = 333 (0%) number of secondary alignments = 0 number of mapped bases = 504,309,617 bp number of sequenced bases = 504,208,044 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,565,423 duplication rate = 17.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7144 >>>>>>> ACTG content number of A's = 145,419,876 bp (28.84%) number of C's = 98,959,756 bp (19.63%) number of T's = 148,373,590 bp (29.43%) number of G's = 111,256,616 bp (22.07%) number of N's = 198,206 bp (0.04%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 2,400,402 number of insertions = 19,584 mapped reads with insertion percentage = 0.18% number of deletions = 67,118 mapped reads with deletion percentage = 0.63% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 0.1629X std coverageData = 1.1381X There is a 6.65% of reference with a coverageData >= 1X There is a 3% of reference with a coverageData >= 2X There is a 1.74% of reference with a coverageData >= 3X There is a 1.13% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 43509202 0.17456005455649395 1.2874971904882282 chr2 243199373 41918576 0.17236301016285926 1.2381907005641446 chr3 198022430 36213368 0.18287508137335756 1.118956237520147 chr4 191154276 31767023 0.166185259700913 1.1228853597283204 chr5 180915260 24711607 0.13659216475160801 0.903493414124787 chr6 171115067 24553517 0.14349126251985747 1.0117813802852105 chr7 159138663 32613272 0.2049361945437483 1.3118092933838563 chr8 146364022 25108816 0.17155046477200525 1.1189904514035207 chr9 141213431 24537469 0.17376158079467668 1.1547055084774942 chr10 135534747 21980444 0.16217571129564287 1.1568813408523342 chr11 135006516 22403275 0.16594217570950429 1.108132988160688 chr12 133851895 18442401 0.13778214346535775 0.9254098201670384 chr13 115169878 15942762 0.1384282268667507 0.9360666480971294 chr14 107349540 11620430 0.10824853092057964 0.9289109568174371 chr15 102531392 13102928 0.12779430518216314 0.8633501771047243 chr16 90354753 14487493 0.16034013174713677 1.127998394581572 chr17 81195210 10092166 0.12429509080646506 0.8619359566947656 chr18 78077248 18647630 0.2388356464613097 1.5035264408990303 chr19 59128983 10276815 0.1738033444613786 1.5140142703874229 chr20 63025520 10172433 0.16140180993349995 1.1627567661278675 chr21 48129895 6189970 0.12860967180584956 1.1653042862077971 chr22 51304566 6766571 0.13189022980917528 0.9776017524742538 chrMT 16571 27899 1.6836038863074045 3.538286289659809 chrX 155270560 37835872 0.2436770499185422 1.4517083982565722 chrY 59373566 1387678 0.02337198341767109 0.5216328189158813