BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818975.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,489,507 number of mapped reads = 1,452,253 (97.5%) number of supplementary alignments = 22,536 (1.51%) number of secondary alignments = 0 number of mapped bases = 134,358,854 bp number of sequenced bases = 134,277,517 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 571,396 duplication rate = 33.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1925 >>>>>>> ACTG content number of A's = 38,392,669 bp (28.59%) number of C's = 27,568,708 bp (20.53%) number of T's = 39,123,407 bp (29.14%) number of G's = 29,186,499 bp (21.74%) number of N's = 6,234 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 865,523 number of insertions = 22,108 mapped reads with insertion percentage = 1.48% number of deletions = 43,291 mapped reads with deletion percentage = 2.91% homopolymer indels = 40.79% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.5484X There is a 2.27% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 13491941 0.054130019599830805 0.9811895011219609 chr2 243199373 10613833 0.04364251794349815 0.7413183054503591 chr3 198022430 7247241 0.036598081338563515 0.32505101472143316 chr4 191154276 7307043 0.03822589351859437 0.384032208709055 chr5 180915260 7274911 0.04021170464006187 0.3456621805223258 chr6 171115067 5609132 0.032779883725843964 0.3691709405860358 chr7 159138663 6593929 0.041435116241990796 0.6189221040886741 chr8 146364022 12313659 0.08413036777576391 0.5489009690940562 chr9 141213431 5655838 0.040051700181408384 0.4872505747211454 chr10 135534747 7212748 0.05321696583090977 0.6700983385780649 chr11 135006516 4383402 0.0324680773185792 0.3667440935839943 chr12 133851895 6226906 0.04652086546850906 0.3708687822261162 chr13 115169878 2881828 0.025022410807798198 0.2653808149223331 chr14 107349540 3178484 0.02960873423397995 0.3001460151029795 chr15 102531392 3556531 0.034687239982073 0.3184543050297457 chr16 90354753 4367974 0.04834249284041538 0.6140533239958883 chr17 81195210 4862716 0.05988919789726512 0.46471248391126607 chr18 78077248 3205558 0.04105623702310819 0.6007565002843999 chr19 59128983 2924911 0.049466621132313406 0.9040183877896346 chr20 63025520 4036618 0.06404735732446158 0.4628002905467643 chr21 48129895 1916125 0.039811535013737305 0.38115298838983386 chr22 51304566 1080420 0.021058944344251932 0.2700011603794696 chrMT 16571 28841 1.7404501840564843 2.7807787971959828 chrX 155270560 7866864 0.05066552216981764 0.4312418055883449 chrY 59373566 521401 0.008781702618299869 0.540522134249347