BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238624.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 = 3,178,599 number of mapped reads = 2,768,418 (87.1%) number of supplementary alignments = 29,452 (0.93%) number of secondary alignments = 0 number of mapped bases = 170,255,377 bp number of sequenced bases = 170,160,963 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 805,852 duplication rate = 19.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5038 >>>>>>> ACTG content number of A's = 42,699,706 bp (25.09%) number of C's = 30,193,653 bp (17.74%) number of T's = 56,702,710 bp (33.32%) number of G's = 40,556,436 bp (23.83%) number of N's = 8,458 bp (0%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,060,679 number of insertions = 10,763 mapped reads with insertion percentage = 0.39% number of deletions = 56,127 mapped reads with deletion percentage = 2.01% homopolymer indels = 40.42% >>>>>>> Coverage mean coverageData = 0.055X std coverageData = 0.8369X There is a 2.38% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.43% 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% 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 21035538 0.0843951277457399 0.6734643034522657 chr2 243199373 16062553 0.06604685202046141 2.204616398655507 chr3 198022430 28319213 0.14301012769109034 0.7818102283517502 chr4 191154276 7402352 0.03872449078774466 0.3889836859636458 chr5 180915260 7385637 0.04082373703578128 0.4065472003550207 chr6 171115067 11225365 0.06560126584294299 0.856504244428526 chr7 159138663 12079637 0.0759063622395772 0.7466021061704979 chr8 146364022 19873831 0.13578358074909966 0.89544919951251 chr9 141213431 4116404 0.029150230051417703 0.4186076891076805 chr10 135534747 4427756 0.03266878861698838 0.4459421428087339 chr11 135006516 1623524 0.012025523271780452 0.23576748213476534 chr12 133851895 2276051 0.01700424936083273 0.25867434214434804 chr13 115169878 4387735 0.03809793911564272 0.5191759604746359 chr14 107349540 1025636 0.009554172286159773 0.18953649181467228 chr15 102531392 6429488 0.06270750717984985 0.5936409135374452 chr16 90354753 4531320 0.05015032247390461 0.486655892287582 chr17 81195210 1034220 0.012737450891499634 0.21395739546706818 chr18 78077248 8276114 0.10599904853203843 1.3742032174364955 chr19 59128983 917047 0.015509263874875034 0.3923115438046708 chr20 63025520 1623287 0.025756027082362826 0.34213159913524077 chr21 48129895 1516722 0.03151309596665441 0.36507549604121364 chr22 51304566 1539724 0.030011441866597214 0.3424920718114608 chrMT 16571 57965 3.497978395993 4.4144597407920045 chrX 155270560 2709428 0.01744972131226937 0.27052236462740525 chrY 59373566 378830 0.006380448834755858 0.2747845400272776