BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013190.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 = 3,046,076 number of mapped reads = 2,761,242 (90.65%) number of supplementary alignments = 26,110 (0.86%) number of secondary alignments = 0 number of mapped bases = 180,363,813 bp number of sequenced bases = 180,284,528 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,191 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8107 >>>>>>> ACTG content number of A's = 49,381,045 bp (27.39%) number of C's = 34,833,150 bp (19.32%) number of T's = 54,312,206 bp (30.13%) number of G's = 41,737,282 bp (23.15%) number of N's = 20,845 bp (0.01%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,392,892 number of insertions = 12,851 mapped reads with insertion percentage = 0.46% number of deletions = 46,153 mapped reads with deletion percentage = 1.65% homopolymer indels = 45.01% >>>>>>> Coverage mean coverageData = 0.0583X std coverageData = 0.689X There is a 5.01% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.08% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 15609769 0.06262680083753934 1.3738667143208925 chr2 243199373 25857694 0.10632302904826979 0.7924001329348166 chr3 198022430 9566097 0.04830814872840415 0.25930192865485174 chr4 191154276 10530785 0.0550905018729479 0.27885989676100387 chr5 180915260 6895674 0.038115491197370524 0.2227246070589493 chr6 171115067 11293166 0.06599749629294771 0.43546651851010715 chr7 159138663 11292793 0.07096196981370895 1.4637725625277154 chr8 146364022 10804664 0.0738204912133393 0.5151469990852102 chr9 141213431 6060661 0.04291844590901555 0.4791006323285931 chr10 135534747 5305874 0.0391477028396268 0.8077591394041749 chr11 135006516 6720888 0.04978195274663632 0.4243729729394888 chr12 133851895 10199454 0.07619954876245869 0.321792874841846 chr13 115169878 2188249 0.01900018510048261 0.15441630709143528 chr14 107349540 6441149 0.06000164509321605 0.2992477702487352 chr15 102531392 2207345 0.02152847978500087 0.17522111918413008 chr16 90354753 5097120 0.05641230627900671 0.322560355188396 chr17 81195210 6714896 0.0827006420698955 0.365016750797136 chr18 78077248 6134560 0.07857039223513616 1.0536303700454728 chr19 59128983 3329983 0.05631727168383735 1.0344072473254382 chr20 63025520 3287114 0.05215528566840861 0.2697323581901697 chr21 48129895 2374015 0.04932516474428211 0.2654460096468236 chr22 51304566 1979245 0.03857834018126184 0.2158836658594552 chrMT 16571 507116 30.60261903325086 16.997179291837707 chrX 155270560 9605355 0.06186204905810863 0.3518067940247833 chrY 59373566 360147 0.0060657801823794785 0.12404053152837824