BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230355.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 = 2,346,834 number of mapped reads = 1,854,673 (79.03%) number of supplementary alignments = 7,643 (0.33%) number of secondary alignments = 0 number of mapped bases = 116,527,568 bp number of sequenced bases = 116,464,066 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,962 duplication rate = 3.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8863 >>>>>>> ACTG content number of A's = 29,856,243 bp (25.64%) number of C's = 19,567,849 bp (16.8%) number of T's = 39,007,156 bp (33.49%) number of G's = 27,821,348 bp (23.89%) number of N's = 211,470 bp (0.18%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,128,833 number of insertions = 10,923 mapped reads with insertion percentage = 0.58% number of deletions = 39,212 mapped reads with deletion percentage = 2.09% homopolymer indels = 48.48% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.4227X There is a 3.21% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12493221 0.05012312888079023 0.7328881730994182 chr2 243199373 10051412 0.04132992563266189 0.5033742578880813 chr3 198022430 6774590 0.03421122546572123 0.21177082331481042 chr4 191154276 7434532 0.03889283648564576 0.24482206253064193 chr5 180915260 8282092 0.04577884695851527 0.24621805245422176 chr6 171115067 4288805 0.025063865357923158 0.24588443021012898 chr7 159138663 6666405 0.04189054296629349 0.6821224833474748 chr8 146364022 5573657 0.038080786000811044 0.4847314311050288 chr9 141213431 4432028 0.03138531489968543 0.48498214422104047 chr10 135534747 4971978 0.03668415745816089 0.35646170951259637 chr11 135006516 5964541 0.04417965278061097 0.3996039561724038 chr12 133851895 6164171 0.046052175802217814 0.253101249305912 chr13 115169878 3503173 0.030417441268801203 0.19494913628096344 chr14 107349540 3034159 0.02826429437890465 0.24186797176291033 chr15 102531392 3369553 0.03286362287951772 0.20820073249687399 chr16 90354753 3506174 0.03880453306092265 0.257287895535664 chr17 81195210 3316456 0.04084546366713012 0.28285484454474213 chr18 78077248 2728920 0.03495153927556463 0.8381622628943227 chr19 59128983 2251886 0.03808430123007527 0.5828146476991881 chr20 63025520 2722301 0.04319363013585608 0.257076940976555 chr21 48129895 1867316 0.03879742517618208 0.24357066437576533 chr22 51304566 1439808 0.02806393489421585 0.1884617024014959 chrMT 16571 76370 4.608653672077726 4.354677267899618 chrX 155270560 5303840 0.034158696922327064 0.29858614583611237 chrY 59373566 310180 0.0052242103834558296 0.12316844589087923