BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008657.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 = 1,567,399 number of mapped reads = 1,374,487 (87.69%) number of supplementary alignments = 12,674 (0.81%) number of secondary alignments = 0 number of mapped bases = 89,787,615 bp number of sequenced bases = 89,732,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,479 duplication rate = 4.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0543 >>>>>>> ACTG content number of A's = 24,300,550 bp (27.08%) number of C's = 17,350,261 bp (19.34%) number of T's = 27,564,485 bp (30.72%) number of G's = 20,399,643 bp (22.73%) number of N's = 117,579 bp (0.13%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 815,417 number of insertions = 6,734 mapped reads with insertion percentage = 0.49% number of deletions = 31,478 mapped reads with deletion percentage = 2.26% homopolymer indels = 44.67% >>>>>>> Coverage mean coverageData = 0.029X std coverageData = 0.3835X There is a 2.16% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% 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% 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 9553715 0.03832975405104407 0.683696707860801 chr2 243199373 8357990 0.034366823799336026 0.5077384610981935 chr3 198022430 7121656 0.035963885505293516 0.26808340587384105 chr4 191154276 3394252 0.017756610372660457 0.1734390464107481 chr5 180915260 1593552 0.008808278527748296 0.11978306437311804 chr6 171115067 3868568 0.022607991615373062 0.20325170906389584 chr7 159138663 4394554 0.027614621847112036 0.5659157837279086 chr8 146364022 7844277 0.053594297921110694 0.469019060768424 chr9 141213431 1468680 0.010400427137840734 0.25094430593224176 chr10 135534747 7032291 0.05188552128259774 0.6764316155364272 chr11 135006516 4170274 0.030889427588813564 0.27411968110673 chr12 133851895 3382617 0.025271341881263617 0.2029922042870168 chr13 115169878 1078479 0.009364245397568277 0.12235826633137196 chr14 107349540 2715087 0.025292022676575977 0.2022477450941693 chr15 102531392 1465287 0.01429110608388112 0.1517639440811268 chr16 90354753 2247181 0.024870645155767288 0.29325728500236864 chr17 81195210 4561097 0.05617445905983863 0.4100601397547571 chr18 78077248 1804777 0.023115274247371014 0.3852493497070694 chr19 59128983 3384684 0.05724238483858246 0.4738837644003931 chr20 63025520 2740493 0.0434822751164925 0.2688263607028886 chr21 48129895 1345741 0.02796060535764726 0.21648076227092186 chr22 51304566 881075 0.01717342273200401 0.1610710864555303 chrMT 16571 80519 4.859030837004405 4.080963788073874 chrX 155270560 5050228 0.03252534157151233 0.27120068496524674 chrY 59373566 250541 0.004219739808115955 0.13691631285530848