BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525007.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,314,452 number of mapped reads = 1,212,278 (92.23%) number of supplementary alignments = 4,080 (0.31%) number of secondary alignments = 0 number of mapped bases = 70,235,383 bp number of sequenced bases = 70,212,301 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,461 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5413 >>>>>>> ACTG content number of A's = 16,525,807 bp (23.54%) number of C's = 13,167,211 bp (18.75%) number of T's = 22,504,899 bp (32.05%) number of G's = 18,013,768 bp (25.66%) number of N's = 616 bp (0%) GC percentage = 44.41% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 333,997 number of insertions = 4,284 mapped reads with insertion percentage = 0.35% number of deletions = 13,878 mapped reads with deletion percentage = 1.14% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0227X std coverageData = 0.2225X There is a 2.09% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% 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 7626155 0.03059633299770194 0.4204063268713885 chr2 243199373 5830267 0.02397319914143035 0.23771135193377266 chr3 198022430 3904404 0.01971697852611949 0.15071658534425267 chr4 191154276 4557616 0.023842605540249594 0.1753008310268051 chr5 180915260 3103995 0.017157176238201243 0.14083093922206846 chr6 171115067 5251025 0.030687098991697793 0.2543014445823458 chr7 159138663 4519087 0.028397165810045796 0.2819755234363281 chr8 146364022 4113464 0.028104338373538273 0.22348805280393022 chr9 141213431 2001423 0.014173035707913647 0.16684844524068349 chr10 135534747 3652035 0.026945378073417587 0.21994141469659945 chr11 135006516 3046658 0.022566747815342483 0.19917412868404877 chr12 133851895 3264625 0.024389830267251725 0.16761134284640303 chr13 115169878 1343175 0.011662554682918045 0.1164587351527669 chr14 107349540 1618134 0.015073506602822891 0.1335864505003024 chr15 102531392 2016720 0.019669293088306068 0.1530447204706998 chr16 90354753 2324138 0.025722365706649656 0.17640431307960866 chr17 81195210 1988827 0.024494388277338033 0.21328638324453444 chr18 78077248 1410299 0.018062867687139793 0.2572130004633639 chr19 59128983 1818588 0.03075628748764375 0.2614962675325091 chr20 63025520 1588090 0.02519757076181204 0.17039307207749027 chr21 48129895 1042319 0.021656373860778212 0.16529201992922438 chr22 51304566 1005260 0.019593967523280482 0.14821290984068558 chrMT 16571 12996 0.784261661939533 1.0531537795760153 chrX 155270560 2994477 0.01928554260382651 0.1667292403480174 chrY 59373566 201606 0.0033955514816138887 0.0943216265683996