BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230331.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,491,430 number of mapped reads = 2,879,788 (82.48%) number of supplementary alignments = 40,888 (1.17%) number of secondary alignments = 0 number of mapped bases = 185,728,237 bp number of sequenced bases = 185,644,757 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 790,932 duplication rate = 14.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0511 >>>>>>> ACTG content number of A's = 50,340,094 bp (27.12%) number of C's = 34,857,279 bp (18.78%) number of T's = 57,930,417 bp (31.2%) number of G's = 42,440,127 bp (22.86%) number of N's = 76,840 bp (0.04%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,726,768 number of insertions = 17,212 mapped reads with insertion percentage = 0.59% number of deletions = 49,519 mapped reads with deletion percentage = 1.7% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 0.06X std coverageData = 0.929X There is a 1.74% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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% 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 16099720 0.06459249704336745 1.711225951589899 chr2 243199373 18884824 0.07765161466925329 1.0668478879684935 chr3 198022430 10529341 0.05317246637161255 0.5981442504247034 chr4 191154276 8278409 0.04330747484822155 0.6582666563281027 chr5 180915260 14794065 0.0817734501777241 0.7514008229178071 chr6 171115067 9833668 0.057468159715006274 0.7151427856736124 chr7 159138663 8988035 0.056479266763727935 1.202642807405205 chr8 146364022 10350577 0.07071804162364437 1.0661812269741162 chr9 141213431 10902904 0.07720868987313254 0.8464430481388976 chr10 135534747 11793830 0.08701702154651161 1.0716277448747422 chr11 135006516 6171410 0.045711941785091324 0.6675160038234116 chr12 133851895 6143898 0.045900717356298915 0.5657989855624422 chr13 115169878 4324582 0.03754959261135972 0.5115903114429863 chr14 107349540 5948016 0.05540793188308026 0.6359785746942513 chr15 102531392 7114597 0.06938945098882496 0.6910638464238367 chr16 90354753 3964758 0.04387990524416574 0.5951754419076104 chr17 81195210 4298729 0.05294313543865457 0.616482046067875 chr18 78077248 4028953 0.05160213894833998 1.3977280714875335 chr19 59128983 5609072 0.09486163494474444 1.2147610108936904 chr20 63025520 2396596 0.038025802881118634 0.5606148156714638 chr21 48129895 2044477 0.04247831830923379 0.5981115121838875 chr22 51304566 2012387 0.03922432556977482 0.5001524123167065 chrMT 16571 37501 2.263049906463098 5.073540072605538 chrX 155270560 10390146 0.06691639419604077 0.7057335084398055 chrY 59373566 787742 0.013267554116591211 0.44451799650724705