BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240234.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 = 3,409,637 number of mapped reads = 2,209,184 (64.79%) number of supplementary alignments = 17,855 (0.52%) number of secondary alignments = 0 number of mapped bases = 147,505,302 bp number of sequenced bases = 147,434,915 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 350,886 duplication rate = 11.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1171 >>>>>>> ACTG content number of A's = 41,970,897 bp (28.47%) number of C's = 27,348,607 bp (18.55%) number of T's = 46,880,632 bp (31.8%) number of G's = 31,177,496 bp (21.15%) number of N's = 57,283 bp (0.04%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,258,971 number of insertions = 10,783 mapped reads with insertion percentage = 0.48% number of deletions = 39,931 mapped reads with deletion percentage = 1.79% homopolymer indels = 48.5% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.5837X There is a 1.81% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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% 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 11826113 0.047446674164956244 0.9680114928616868 chr2 243199373 15582802 0.06407418657284121 0.6389460312239472 chr3 198022430 9623611 0.0485985905738052 0.472496225617344 chr4 191154276 9532065 0.04986582146872822 0.4812119394703426 chr5 180915260 7964082 0.044021062678737 0.45105715303434546 chr6 171115067 7684175 0.04490647804848184 0.5006072284777937 chr7 159138663 8736217 0.054896885742969956 0.7156418811910168 chr8 146364022 8478612 0.05792825234059228 0.7718387186874159 chr9 141213431 5172885 0.036631678469734225 0.4663070776575391 chr10 135534747 6933398 0.05115587075246468 0.5535852851643678 chr11 135006516 6422607 0.047572570497263995 0.5438515196897877 chr12 133851895 7239385 0.05408503928913371 0.5108365958564978 chr13 115169878 3999370 0.034725833433634445 0.39582019733604357 chr14 107349540 4785979 0.044583134683204045 0.45913602519183677 chr15 102531392 4381626 0.04273448272310591 0.4433282755619825 chr16 90354753 4376680 0.048438846377013504 0.4643314623897145 chr17 81195210 3449034 0.04247829397817925 0.45565579255789523 chr18 78077248 3467244 0.04440786642480022 0.7417366763538514 chr19 59128983 2634694 0.044558419007477264 0.6432417015644629 chr20 63025520 3010129 0.04776047861247317 0.4657701692141098 chr21 48129895 2326914 0.04834654220625247 0.47401819606172046 chr22 51304566 1351804 0.026348609985317874 0.3361126500593425 chrMT 16571 40620 2.4512702914730555 3.8096062340187724 chrX 155270560 8064474 0.0519382038681383 0.5137808996236245 chrY 59373566 420782 0.007087025899707624 0.163471973871609