BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237835.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 = 1,942,211 number of mapped reads = 1,475,520 (75.97%) number of supplementary alignments = 9,882 (0.51%) number of secondary alignments = 0 number of mapped bases = 94,302,325 bp number of sequenced bases = 94,266,706 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,991 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4971 >>>>>>> ACTG content number of A's = 26,062,253 bp (27.65%) number of C's = 18,228,118 bp (19.34%) number of T's = 28,560,002 bp (30.3%) number of G's = 21,328,853 bp (22.63%) number of N's = 87,480 bp (0.09%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 726,384 number of insertions = 7,334 mapped reads with insertion percentage = 0.49% number of deletions = 21,306 mapped reads with deletion percentage = 1.43% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.0305X std coverageData = 0.3029X There is a 2.56% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 8086213 0.03244209770695015 0.5045750807659628 chr2 243199373 9883138 0.040638007730389995 0.35808698542112166 chr3 198022430 7143369 0.03607353470008423 0.2256233732390448 chr4 191154276 8606620 0.04502447018239864 0.2673961067194008 chr5 180915260 4987100 0.027565944409553955 0.19258139943236144 chr6 171115067 4895295 0.028608205494844004 0.2310561240624656 chr7 159138663 4295777 0.026993924160340594 0.27199489405523997 chr8 146364022 4932151 0.03369783730048085 0.32196325347896815 chr9 141213431 3599500 0.02548978503326642 0.32124881302202163 chr10 135534747 4711678 0.0347636167425022 0.4358285735060981 chr11 135006516 5133987 0.03802769786311647 0.300269524559617 chr12 133851895 4047318 0.030237285770216404 0.20658934631491518 chr13 115169878 2531348 0.021979253985143582 0.1691789625776495 chr14 107349540 2866903 0.026706243920560816 0.2221173587087089 chr15 102531392 1948959 0.01900841256500253 0.15689239128513338 chr16 90354753 2461315 0.027240570288538112 0.23478177124063404 chr17 81195210 1982886 0.02442121893643726 0.20010879161464987 chr18 78077248 1995210 0.025554307446901816 0.5421312750602666 chr19 59128983 1609795 0.02722514270201468 0.34765076054242994 chr20 63025520 1594978 0.02530685982440129 0.19345928812327337 chr21 48129895 1138244 0.023649417892974835 0.20811300101924074 chr22 51304566 869855 0.016954728746755212 0.14937162282587693 chrMT 16571 20136 1.2151348741777805 1.2653376527662485 chrX 155270560 4691861 0.030217325164538598 0.22993837011297424 chrY 59373566 268689 0.004525397716552851 0.13990582151733938