BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524893.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 836,023 number of mapped reads = 767,926 (91.85%) number of supplementary alignments = 2,568 (0.31%) number of secondary alignments = 0 number of mapped bases = 44,854,349 bp number of sequenced bases = 44,840,820 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,831 duplication rate = 1.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6672 >>>>>>> ACTG content number of A's = 12,243,580 bp (27.3%) number of C's = 7,693,652 bp (17.16%) number of T's = 14,330,874 bp (31.96%) number of G's = 10,567,268 bp (23.57%) number of N's = 5,446 bp (0.01%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 222,077 number of insertions = 3,706 mapped reads with insertion percentage = 0.48% number of deletions = 8,442 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 0.1736X There is a 1.36% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 3646723 0.014630747900924989 0.32211049271802966 chr2 243199373 3862490 0.015881989958913257 0.18260013227250468 chr3 198022430 3007727 0.015188819771578401 0.1286080992815136 chr4 191154276 2980133 0.015590197940432156 0.13850640066149622 chr5 180915260 2779568 0.015363922313684318 0.13003983716781697 chr6 171115067 2581588 0.015086853806976564 0.1349810017204207 chr7 159138663 2352137 0.014780424540829527 0.20810287668149766 chr8 146364022 2296419 0.0156897779155044 0.17241631142276032 chr9 141213431 1884744 0.013346775775173963 0.1566340475110136 chr10 135534747 2097762 0.01547766935367504 0.1678098777468463 chr11 135006516 2030845 0.015042570241572637 0.16059121534454937 chr12 133851895 2002614 0.014961416870489581 0.1296248126902323 chr13 115169878 1477789 0.012831384609090234 0.11819892824977611 chr14 107349540 1380650 0.012861256787872588 0.1225536702678455 chr15 102531392 1249722 0.012188676810317762 0.11518063822114717 chr16 90354753 1224673 0.013554051771908446 0.1279440458528147 chr17 81195210 1123804 0.01384076720781928 0.1295328061530993 chr18 78077248 1256489 0.01609289558976259 0.2726258206398641 chr19 59128983 798210 0.013499471147677274 0.20929410446412888 chr20 63025520 896558 0.014225316982707957 0.12688210378517178 chr21 48129895 600502 0.012476694578286531 0.12500447752564256 chr22 51304566 474662 0.009251847096806159 0.10026738859298251 chrMT 16571 8249 0.4977973568281938 0.7530305918929247 chrX 155270560 2696639 0.017367355408520455 0.15032961050885096 chrY 59373566 143652 0.0024194605390553767 0.07470032776816683