BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504712.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,279,957 number of mapped reads = 2,060,792 (90.39%) number of secondary alignments = 0 number of mapped bases = 65,938,560 bp number of sequenced bases = 65,938,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 374,742 duplication rate = 8.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.9925 >>>>>>> ACTG content number of A's = 18,742,684 bp (28.42%) number of C's = 13,441,029 bp (20.38%) number of T's = 20,110,077 bp (30.5%) number of G's = 13,644,677 bp (20.69%) number of N's = 93 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 32,080 >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 1.0797X There is a 1.08% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 4924514 0.019757278759197153 0.34464333746594034 chr2 243199373 4258368 0.017509781984511943 0.3605114376684778 chr3 198022430 4169488 0.021055634960140627 0.3269899491294097 chr4 191154276 3994376 0.020896085003089336 0.40580196433386345 chr5 180915260 3586504 0.019824220466532233 0.29810553709876897 chr6 171115067 4456816 0.026045725126005413 0.5431722507817172 chr7 159138663 3516714 0.022098426200803257 0.3679477436730583 chr8 146364022 10283642 0.07026072295280325 4.698917277168425 chr9 141213431 2097734 0.014855060068613445 0.19858155624809246 chr10 135534747 2973866 0.021941723918221502 0.448955594980434 chr11 135006516 2937996 0.021761882959782475 0.2875650373211417 chr12 133851895 1980256 0.014794381506515093 0.20049392059549187 chr13 115169878 1940958 0.016853000399983057 0.2908673193734399 chr14 107349540 1655340 0.015420094021828132 0.29679246348438715 chr15 102531392 1191458 0.011620421577812968 0.21655445103228482 chr16 90354753 1289846 0.014275353063053584 0.27678074403217856 chr17 81195210 1007518 0.012408589127363548 0.20430369725148842 chr18 78077248 1565334 0.020048529374395982 0.4072945568795146 chr19 59128983 503724 0.008519070926689201 0.12059211330448315 chr20 63025520 884858 0.014039677895557228 0.23303726046741222 chr21 48129895 506114 0.010515584960241447 0.16598814214467994 chr22 51304566 342490 0.006675624153998301 0.1266874700125399 chrMT 16571 96 0.005793253273791563 0.07589263133069815 chrX 155270560 5698616 0.03670120079427806 0.6759134330299201 chrY 59373566 171934 0.002895800464469323 0.06868103272886501