BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549101.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,866,452 number of mapped reads = 10,620,808 (82.55%) number of secondary alignments = 0 number of mapped bases = 419,818,424 bp number of sequenced bases = 419,771,289 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 464,927 duplication rate = 2.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7234 >>>>>>> ACTG content number of A's = 127,179,261 bp (30.3%) number of C's = 83,132,958 bp (19.8%) number of T's = 126,952,285 bp (30.24%) number of G's = 82,505,069 bp (19.65%) number of N's = 1,716 bp (0%) GC percentage = 39.46% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 1,538,591 number of insertions = 16,032 mapped reads with insertion percentage = 0.15% number of deletions = 38,065 mapped reads with deletion percentage = 0.36% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.1356X std coverageData = 1.2936X There is a 10.4% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 32489490 0.13034868226065524 1.6205715457962309 chr2 243199373 36505866 0.15010674390184386 0.8873748466897916 chr3 198022430 29280006 0.1478620679485652 0.47801275220609574 chr4 191154276 29265095 0.15309673219133219 0.5131028374949924 chr5 180915260 26982231 0.14914292470408522 0.49800827957106847 chr6 171115067 25600577 0.14961030287297844 0.5576554789448648 chr7 159138663 28847089 0.1812701480343592 1.8467466551860845 chr8 146364022 22468147 0.15350867442000193 4.286710292926054 chr9 141213431 17664417 0.1250902047695449 0.8946624346180404 chr10 135534747 19349191 0.14276184836940745 0.73288108332531 chr11 135006516 19293529 0.14290813193046178 0.7856889038222457 chr12 133851895 19138192 0.1429803590005207 0.5128477294531689 chr13 115169878 14300993 0.12417303246600643 0.4281943870016803 chr14 107349540 12962353 0.12074903162137443 0.7047911973741972 chr15 102531392 11730660 0.11441042368760584 0.4199160809407193 chr16 90354753 10471583 0.11589410243863983 0.5450302455199482 chr17 81195210 9374312 0.11545400276691199 0.47249670233366636 chr18 78077248 11537986 0.14777654560775502 1.7503707083703275 chr19 59128983 6751361 0.11418023205303565 1.4609025562623903 chr20 63025520 7999115 0.12691866723194034 0.48997162554641915 chr21 48129895 5534989 0.11500106119076303 0.5454911919438188 chr22 51304566 3830577 0.0746634714734747 0.5151518472489424 chrMT 16571 84547 5.102106088950577 5.183011608056169 chrX 155270560 15101655 0.097260259768497 0.5479087999438842 chrY 59373566 3254463 0.054813332249573826 0.3939190864044011