BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818976.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,526,013 number of mapped reads = 1,485,477 (97.34%) number of supplementary alignments = 23,256 (1.52%) number of secondary alignments = 0 number of mapped bases = 137,298,292 bp number of sequenced bases = 137,215,253 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 568,851 duplication rate = 32.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2596 >>>>>>> ACTG content number of A's = 39,396,586 bp (28.71%) number of C's = 29,680,579 bp (21.63%) number of T's = 38,855,705 bp (28.32%) number of G's = 29,275,630 bp (21.34%) number of N's = 6,753 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 864,272 number of insertions = 18,930 mapped reads with insertion percentage = 1.24% number of deletions = 44,317 mapped reads with deletion percentage = 2.92% homopolymer indels = 41.52% >>>>>>> Coverage mean coverageData = 0.0444X std coverageData = 0.5384X There is a 2.35% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 13796981 0.055353848045176984 0.9510587295569292 chr2 243199373 11067718 0.04550882620902152 0.7340101203622282 chr3 198022430 7355179 0.03714316100453873 0.3165440178184415 chr4 191154276 7577612 0.039641341844741156 0.3824271775463045 chr5 180915260 7534677 0.04164754813938858 0.3455782292567245 chr6 171115067 5780697 0.033782513143626326 0.3530064014843536 chr7 159138663 6705161 0.04213407900756336 0.6003209299575817 chr8 146364022 12571772 0.08589386809826803 0.5472726536844775 chr9 141213431 5954804 0.04216882174614113 0.49319014070604583 chr10 135534747 7250154 0.0534929540983317 0.6704715739970005 chr11 135006516 4735823 0.03507847724920181 0.37376142467080326 chr12 133851895 6436548 0.04808708909201472 0.37346424198553446 chr13 115169878 2884993 0.02504989195178274 0.261714725935179 chr14 107349540 3118842 0.029053147316700192 0.2966725859529058 chr15 102531392 3547611 0.03460024223605586 0.31600971599018934 chr16 90354753 4404104 0.048742361124046236 0.6109433270652479 chr17 81195210 4932225 0.06074527056460596 0.4729568773374709 chr18 78077248 3144342 0.04027219299532688 0.5747280326955359 chr19 59128983 2789719 0.047180229702242636 0.8315144752665458 chr20 63025520 3947522 0.06263370774251446 0.44553972789182894 chr21 48129895 1879235 0.03904506751988551 0.3611844628819193 chr22 51304566 1093887 0.021321435600878097 0.2817155020733503 chrMT 16571 19867 1.1989016957335104 1.8592597566089015 chrX 155270560 8258999 0.05319101702215797 0.43117829456312934 chrY 59373566 509820 0.008586649486406122 0.5425826728561455