BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237336.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 = 3,098,336 number of mapped reads = 2,791,099 (90.08%) number of supplementary alignments = 25,992 (0.84%) number of secondary alignments = 0 number of mapped bases = 166,473,894 bp number of sequenced bases = 166,377,807 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 812,157 duplication rate = 22.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7435 >>>>>>> ACTG content number of A's = 42,008,171 bp (25.25%) number of C's = 28,194,021 bp (16.95%) number of T's = 56,286,591 bp (33.83%) number of G's = 39,872,564 bp (23.97%) number of N's = 16,460 bp (0.01%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,074,609 number of insertions = 11,562 mapped reads with insertion percentage = 0.41% number of deletions = 55,525 mapped reads with deletion percentage = 1.97% homopolymer indels = 41.23% >>>>>>> Coverage mean coverageData = 0.0538X std coverageData = 0.7009X There is a 2.65% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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 12727561 0.05106330707998517 1.0515102271519612 chr2 243199373 9752030 0.04009891094579426 1.1642020312195245 chr3 198022430 15635583 0.0789586462503263 0.5016746999354715 chr4 191154276 10121150 0.05294754693324255 0.5190632583847068 chr5 180915260 9406214 0.0519923747725869 0.40928933957908753 chr6 171115067 14652701 0.08563068850038787 0.843038150204809 chr7 159138663 10588017 0.06653327859113659 0.5614604304826867 chr8 146364022 13630798 0.09312943040059393 0.9849098846712342 chr9 141213431 9874095 0.06992320015225748 0.618180315862368 chr10 135534747 7121472 0.05254351491134594 0.7008260363498723 chr11 135006516 6221424 0.046082397978479794 0.4522562894504833 chr12 133851895 5074835 0.037913807645382984 0.3844278695000065 chr13 115169878 6033417 0.052387109414147336 0.44744321020574945 chr14 107349540 5439700 0.05067278350703692 0.4366220196841342 chr15 102531392 5904467 0.0575869193310084 0.4478255846292518 chr16 90354753 3116269 0.03448926477614299 0.3706523313036012 chr17 81195210 2576523 0.03173245071969147 0.3356145286660432 chr18 78077248 5552475 0.07111514739863782 1.356059187801214 chr19 59128983 2566592 0.043406665729393654 0.6860469029695865 chr20 63025520 2773299 0.04400279442359222 0.39027448911967944 chr21 48129895 2285160 0.04747901486176107 0.4423506901423399 chr22 51304566 1989767 0.03878342913962083 0.34049916792589663 chrMT 16571 7541 0.45507211393398106 1.1005018942964946 chrX 155270560 2928792 0.018862506839673922 0.2901772812532699 chrY 59373566 494012 0.008320403056134441 0.323298013086996