BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053638.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 4,865,170 number of mapped reads = 3,773,204 (77.56%) number of supplementary alignments = 95 (0%) number of secondary alignments = 0 number of mapped bases = 174,758,500 bp number of sequenced bases = 174,724,747 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,125,613 duplication rate = 19.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7182 >>>>>>> ACTG content number of A's = 54,601,006 bp (31.25%) number of C's = 36,686,850 bp (21%) number of T's = 47,246,058 bp (27.04%) number of G's = 36,190,342 bp (20.71%) number of N's = 491 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 1,032,813 number of insertions = 7,821 mapped reads with insertion percentage = 0.21% number of deletions = 22,436 mapped reads with deletion percentage = 0.59% homopolymer indels = 41.52% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.6681X There is a 2.3% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 13783550 0.05529996252246048 0.6651281508340136 chr2 243199373 14602269 0.06004237930333809 0.7436524101654457 chr3 198022430 11975112 0.06047351302577188 0.6499381633909205 chr4 191154276 11465983 0.05998287477492787 0.6959976070137941 chr5 180915260 10927440 0.06040087497317805 0.7333163942090402 chr6 171115067 10178798 0.05948510659204546 0.7024256486554576 chr7 159138663 9594894 0.06029266439168211 0.7101160596388216 chr8 146364022 8749038 0.05977587852839956 0.6747459983837538 chr9 141213431 7229241 0.05119372108450505 0.6058258426854819 chr10 135534747 8010523 0.05910309479531474 0.6558910340285651 chr11 135006516 7968057 0.05901979575563597 0.7335962682203251 chr12 133851895 7996304 0.05973993868372204 0.6537120582900321 chr13 115169878 5627439 0.048862073119500915 0.5989927043252665 chr14 107349540 5373651 0.05005751305501635 0.6183415141892703 chr15 102531392 5054629 0.04929835537588332 0.5765993709869827 chr16 90354753 5029424 0.05566308171967445 0.642376409240408 chr17 81195210 4654115 0.057320068511430664 0.6307230278905881 chr18 78077248 4593742 0.058835859583575484 0.6646592332502869 chr19 59128983 3329907 0.05631598635816212 0.6656276670549766 chr20 63025520 3700426 0.058713137154600234 0.6496712253543595 chr21 48129895 2216604 0.0460546194833793 0.6623775549826134 chr22 51304566 2013829 0.03925243222991107 0.5741220132615936 chrMT 16571 138925 8.383621990223885 16.360037141551114 chrX 155270560 10099983 0.06504763684757754 0.6852583596434643 chrY 59373566 444617 0.007488467174095624 0.1831993272988592