BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472483.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,359,664 number of mapped reads = 17,109,278 (98.56%) number of supplementary alignments = 58,075 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,592,349 number of mapped paired reads (second in pair) = 8,516,929 number of mapped paired reads (both in pair) = 16,976,064 number of mapped paired reads (singletons) = 133,214 number of mapped bases = 1,678,572,183 bp number of sequenced bases = 1,678,331,541 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,801,656 duplication rate = 45.18% >>>>>>> Insert size mean insert size = 27,920.259 std insert size = 1,626,238.9799 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 54.9148 >>>>>>> ACTG content number of A's = 463,811,525 bp (27.64%) number of C's = 378,132,608 bp (22.53%) number of T's = 460,661,638 bp (27.45%) number of G's = 375,466,256 bp (22.37%) number of N's = 259,514 bp (0.02%) GC percentage = 44.9% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 10,035,764 number of insertions = 90,142 mapped reads with insertion percentage = 0.52% number of deletions = 91,192 mapped reads with deletion percentage = 0.53% homopolymer indels = 44.74% >>>>>>> Coverage mean coverageData = 0.5422X std coverageData = 20.4004X There is a 5.55% of reference with a coverageData >= 1X There is a 2.5% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 198864572 0.7978498557080826 32.259037008467345 chr2 243199373 120244167 0.4944263034757084 29.179764866943795 chr3 198022430 191525803 0.9671924690551469 21.38555424227324 chr4 191154276 86834407 0.454263481921796 20.796898136026467 chr5 180915260 108776151 0.6012547034451378 18.75675458772119 chr6 171115067 116948828 0.6834513760264022 20.700767434647094 chr7 159138663 101691428 0.6390114512901243 21.17082820532896 chr8 146364022 84805553 0.5794152951057877 18.419386565621153 chr9 141213431 118859896 0.8417039027966114 21.112385146535637 chr10 135534747 71496961 0.5275175745154119 28.326077226872602 chr11 135006516 51391114 0.3806565454959226 15.338236290390254 chr12 133851895 75419771 0.5634568789631256 19.887637381987247 chr13 115169878 28941093 0.2512904719756671 7.89209697820519 chr14 107349540 34541452 0.321766185490874 11.097710736849368 chr15 102531392 36330470 0.3543350898815457 12.184858200474876 chr16 90354753 53976079 0.5973795202561176 18.69738074212911 chr17 81195210 49190226 0.6058266983976025 12.89143427291697 chr18 78077248 20651084 0.26449554164614 9.438375301308396 chr19 59128983 20017394 0.33853776920194956 9.836347444154287 chr20 63025520 25814988 0.4095957954809417 13.63811831913566 chr21 48129895 10829844 0.22501283246098916 9.533723436960372 chr22 51304566 12407196 0.24183414786122545 9.257970573955387 chrMT 16571 1752 0.10572687224669604 0.39904890546853106 chrX 155270560 53222432 0.34277220356518323 10.99730294215495 chrY 59373566 5789522 0.0975100939701011 5.0665528841784795