BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237841.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 = 1,825,785 number of mapped reads = 1,433,640 (78.52%) number of supplementary alignments = 9,116 (0.5%) number of secondary alignments = 0 number of mapped bases = 92,924,392 bp number of sequenced bases = 92,888,593 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,607 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3406 >>>>>>> ACTG content number of A's = 27,188,120 bp (29.27%) number of C's = 16,903,261 bp (18.2%) number of T's = 27,544,145 bp (29.65%) number of G's = 21,176,105 bp (22.8%) number of N's = 76,962 bp (0.08%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 787,733 number of insertions = 8,309 mapped reads with insertion percentage = 0.57% number of deletions = 21,648 mapped reads with deletion percentage = 1.49% homopolymer indels = 46.1% >>>>>>> Coverage mean coverageData = 0.03X std coverageData = 0.2869X There is a 2.79% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7672714 0.030783128921472176 0.47577218515521646 chr2 243199373 8873895 0.03648814916969379 0.34359294601059204 chr3 198022430 6266672 0.031646273606479834 0.1908757180428729 chr4 191154276 6257085 0.03273316784187449 0.21763521696380403 chr5 180915260 5506437 0.030436553555515437 0.1827667770605362 chr6 171115067 5266946 0.030780141645855182 0.21306833740343098 chr7 159138663 5224917 0.03283248018741995 0.3698926046106338 chr8 146364022 4821917 0.0329446877320712 0.28021091659900743 chr9 141213431 4377000 0.030995635252287015 0.2970592396840649 chr10 135534747 4462218 0.03292305551726894 0.4055855128879589 chr11 135006516 4061682 0.03008508122674612 0.24397992160031795 chr12 133851895 3925923 0.0293303505340735 0.18166273706561095 chr13 115169878 2784473 0.024177094291964085 0.1604746098307524 chr14 107349540 2747791 0.02559667232854468 0.2016352990014676 chr15 102531392 2612194 0.02547701683402484 0.16575742864625098 chr16 90354753 2443867 0.027047464785831466 0.21329336398999385 chr17 81195210 2186323 0.026926748511396176 0.2086989357919728 chr18 78077248 2486557 0.03184739554344948 0.5194363462403688 chr19 59128983 1503937 0.025434853158221915 0.33902227223599024 chr20 63025520 1751364 0.027788172156294783 0.18443680310185726 chr21 48129895 1234375 0.025646742009306275 0.19516254969566965 chr22 51304566 964475 0.01879900903946834 0.1425397704538743 chrMT 16571 30729 1.8543841651077182 1.7527347949656134 chrX 155270560 5180591 0.03336492764629689 0.21457048994602748 chrY 59373566 280310 0.004721124548928053 0.14198861086035383