BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472663.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,990,548 number of mapped reads = 15,887,274 (99.35%) number of supplementary alignments = 102,861 (0.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,961,913 number of mapped paired reads (second in pair) = 7,925,361 number of mapped paired reads (both in pair) = 15,819,580 number of mapped paired reads (singletons) = 67,694 number of mapped bases = 1,561,492,240 bp number of sequenced bases = 1,561,289,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,324,041 duplication rate = 49.88% >>>>>>> Insert size mean insert size = 19,346.171 std insert size = 1,337,670.5362 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 54.715 >>>>>>> ACTG content number of A's = 421,394,422 bp (26.99%) number of C's = 360,678,745 bp (23.1%) number of T's = 423,250,170 bp (27.11%) number of G's = 355,667,447 bp (22.78%) number of N's = 298,724 bp (0.02%) GC percentage = 45.88% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 8,665,748 number of insertions = 101,354 mapped reads with insertion percentage = 0.63% number of deletions = 79,967 mapped reads with deletion percentage = 0.5% homopolymer indels = 43.76% >>>>>>> Coverage mean coverageData = 0.5044X std coverageData = 26.6349X There is a 2.89% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 166929766 0.6697265801395937 30.303056083641668 chr2 243199373 117278075 0.4822301700588677 23.585107311700135 chr3 198022430 159719602 0.8065732856626393 27.40116673944116 chr4 191154276 27793200 0.14539669518038928 9.598278394692345 chr5 180915260 106343566 0.5878087122114519 40.20552986061457 chr6 171115067 97633567 0.5705725901974489 18.746055630400924 chr7 159138663 89401070 0.5617809545126065 24.670737876760956 chr8 146364022 90965117 0.621499161863699 38.01750124905263 chr9 141213431 110522161 0.7826604043067263 32.48520429548919 chr10 135534747 44785017 0.3304319961581512 28.74413794132885 chr11 135006516 20809276 0.15413534558583825 6.880286613557177 chr12 133851895 47144228 0.35221188314143775 13.813932654235524 chr13 115169878 38352232 0.33300575346619715 19.619830679428578 chr14 107349540 29525734 0.2750429484839898 18.926068032778687 chr15 102531392 22170584 0.2162321564892048 11.68297274085253 chr16 90354753 78404445 0.867740128734567 33.34402448700762 chr17 81195210 49831184 0.613720735496589 18.933144266664225 chr18 78077248 7764803 0.09945026494786291 4.288089105041436 chr19 59128983 31514139 0.5329727893341241 15.53023295631581 chr20 63025520 63510106 1.0076887267253012 30.4317797512936 chr21 48129895 12252398 0.2545693897732376 24.73868054026335 chr22 51304566 9799288 0.1910022589412412 6.398086797869049 chrMT 16571 2832 0.17090097157685114 0.5312063830380663 chrX 155270560 137705171 0.886872379413071 49.43221843231344 chrY 59373566 1334679 0.022479347122253024 1.8765731144906075