BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514770.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 73,212,771 number of mapped reads = 72,635,238 (99.21%) number of supplementary alignments = 5,000,995 (6.83%) number of secondary alignments = 0 number of mapped bases = 6,934,662,700 bp number of sequenced bases = 6,929,865,264 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,800,965 duplication rate = 52.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3206 >>>>>>> ACTG content number of A's = 2,044,854,051 bp (29.51%) number of C's = 1,419,380,792 bp (20.48%) number of T's = 2,018,110,936 bp (29.12%) number of G's = 1,446,171,761 bp (20.87%) number of N's = 1,347,724 bp (0.02%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 42,740,255 number of insertions = 3,305,098 mapped reads with insertion percentage = 4.39% number of deletions = 2,234,285 mapped reads with deletion percentage = 2.96% homopolymer indels = 43.96% >>>>>>> Coverage mean coverageData = 2.2401X std coverageData = 180.7973X There is a 3.88% of reference with a coverageData >= 1X There is a 2.01% of reference with a coverageData >= 2X There is a 1.45% of reference with a coverageData >= 3X There is a 1.23% of reference with a coverageData >= 4X There is a 1.09% of reference with a coverageData >= 5X There is a 1% of reference with a coverageData >= 6X There is a 0.94% of reference with a coverageData >= 7X There is a 0.89% of reference with a coverageData >= 8X There is a 0.84% of reference with a coverageData >= 9X There is a 0.81% of reference with a coverageData >= 10X There is a 0.78% of reference with a coverageData >= 11X There is a 0.75% of reference with a coverageData >= 12X There is a 0.73% of reference with a coverageData >= 13X There is a 0.71% of reference with a coverageData >= 14X There is a 0.69% of reference with a coverageData >= 15X There is a 0.67% of reference with a coverageData >= 16X There is a 0.65% of reference with a coverageData >= 17X There is a 0.64% of reference with a coverageData >= 18X There is a 0.62% of reference with a coverageData >= 19X There is a 0.61% of reference with a coverageData >= 20X There is a 0.6% of reference with a coverageData >= 21X There is a 0.58% of reference with a coverageData >= 22X There is a 0.57% of reference with a coverageData >= 23X There is a 0.56% of reference with a coverageData >= 24X There is a 0.55% of reference with a coverageData >= 25X There is a 0.54% of reference with a coverageData >= 26X There is a 0.54% of reference with a coverageData >= 27X There is a 0.53% of reference with a coverageData >= 28X There is a 0.52% of reference with a coverageData >= 29X There is a 0.51% of reference with a coverageData >= 30X There is a 0.5% of reference with a coverageData >= 31X There is a 0.5% of reference with a coverageData >= 32X There is a 0.49% of reference with a coverageData >= 33X There is a 0.48% of reference with a coverageData >= 34X There is a 0.48% of reference with a coverageData >= 35X There is a 0.47% of reference with a coverageData >= 36X There is a 0.46% of reference with a coverageData >= 37X There is a 0.46% of reference with a coverageData >= 38X There is a 0.45% of reference with a coverageData >= 39X There is a 0.45% of reference with a coverageData >= 40X There is a 0.44% of reference with a coverageData >= 41X There is a 0.44% of reference with a coverageData >= 42X There is a 0.43% of reference with a coverageData >= 43X There is a 0.43% of reference with a coverageData >= 44X There is a 0.42% of reference with a coverageData >= 45X There is a 0.42% of reference with a coverageData >= 46X There is a 0.41% of reference with a coverageData >= 47X There is a 0.41% of reference with a coverageData >= 48X There is a 0.4% of reference with a coverageData >= 49X There is a 0.4% of reference with a coverageData >= 50X There is a 0.4% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 603906630 2.4228891690504555 511.2709540052669 chr2 243199373 479034085 1.9697175987373947 71.33846496488903 chr3 198022430 448396798 2.2643737782634017 92.96036263304792 chr4 191154276 434398123 2.2725001610740843 113.76308568151353 chr5 180915260 553836978 3.0613060390815017 237.78441121782507 chr6 171115067 348824576 2.0385380557984414 73.53289011857333 chr7 159138663 414920484 2.60728899048247 104.95895545557194 chr8 146364022 383879592 2.6227729106815607 86.10334908195232 chr9 141213431 428771499 3.036336529490598 133.05745357790815 chr10 135534747 415651617 3.06675318470178 122.26173366248551 chr11 135006516 337387541 2.499046349733223 92.60083522003866 chr12 133851895 178395833 1.3327852623976673 43.134325012572795 chr13 115169878 218076118 1.8935169663025953 76.91960575044648 chr14 107349540 147648769 1.3754019719134334 48.937223545180174 chr15 102531392 248170502 2.4204343387827993 81.99880548529808 chr16 90354753 234399032 2.5942080988257477 148.34449616788248 chr17 81195210 166994583 2.056704859806385 72.4149407242782 chr18 78077248 135927288 1.74093338945553 51.47659089128364 chr19 59128983 124642352 2.1079738848205793 82.10230136154163 chr20 63025520 214142425 3.3977097689951625 135.28287237794103 chr21 48129895 78673440 1.634606516386541 65.19842105447088 chr22 51304566 168076976 3.276062719251928 290.3435841332195 chrMT 16571 3134102 189.1317361655905 318.91409152441366 chrX 155270560 134187623 0.86421806554958 45.47961409526548 chrY 59373566 33185734 0.5589311243323334 23.886708814706857