BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085131.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,257,972 number of mapped reads = 2,029,009 (89.86%) number of supplementary alignments = 18,504 (0.82%) number of secondary alignments = 0 number of mapped bases = 136,345,374 bp number of sequenced bases = 136,289,069 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,617 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8467 >>>>>>> ACTG content number of A's = 38,117,076 bp (27.97%) number of C's = 25,375,841 bp (18.62%) number of T's = 42,711,674 bp (31.34%) number of G's = 30,062,677 bp (22.06%) number of N's = 21,801 bp (0.02%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,246,151 number of insertions = 10,972 mapped reads with insertion percentage = 0.54% number of deletions = 34,304 mapped reads with deletion percentage = 1.67% homopolymer indels = 46.35% >>>>>>> Coverage mean coverageData = 0.044X std coverageData = 0.3841X There is a 3.92% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 10981079 0.04405637569103589 0.6771899305562126 chr2 243199373 11737637 0.04826343446206171 0.4473675035516024 chr3 198022430 9152404 0.04621902680418577 0.23472419994507512 chr4 191154276 8793372 0.046001440218894185 0.2400401156513952 chr5 180915260 8508647 0.047031118325784126 0.23884906281708967 chr6 171115067 8177889 0.04779175290274117 0.28254625977341474 chr7 159138663 7744182 0.04866310834847218 0.536811020028053 chr8 146364022 7123557 0.04867013698216082 0.6157517539174622 chr9 141213431 5506494 0.03899412372467602 0.3384307113558149 chr10 135534747 6391354 0.04715657159119499 0.33385383087868575 chr11 135006516 6313501 0.04676441691155114 0.33757229308854475 chr12 133851895 6211602 0.046406530142886655 0.24033141217029982 chr13 115169878 4424799 0.03841975937492961 0.21499154034238155 chr14 107349540 4185044 0.038985206643642814 0.23260641688326794 chr15 102531392 3909115 0.03812603070872187 0.21794422579563574 chr16 90354753 3780863 0.041844649832643556 0.24793099885283532 chr17 81195210 3462145 0.04263976902085727 0.2533811205685919 chr18 78077248 3667625 0.04697431190197687 0.6145840126692387 chr19 59128983 2588529 0.04377766822067614 0.5224056194828933 chr20 63025520 2694461 0.04275190430796921 0.23292766538500811 chr21 48129895 1776758 0.03691589187967271 0.2185850976839085 chr22 51304566 1423740 0.027750746395554735 0.1798869386781818 chrMT 16571 10226 0.6171021664353389 0.8809389570579085 chrX 155270560 7467647 0.0480944166105925 0.2696252551765718 chrY 59373566 312704 0.005266720883835746 0.11662340781594312