BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240201.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 = 1,874,051 number of mapped reads = 1,528,756 (81.57%) number of supplementary alignments = 10,921 (0.58%) number of secondary alignments = 0 number of mapped bases = 97,372,400 bp number of sequenced bases = 97,326,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 159,200 duplication rate = 8.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0397 >>>>>>> ACTG content number of A's = 27,020,315 bp (27.76%) number of C's = 17,568,623 bp (18.05%) number of T's = 31,105,217 bp (31.96%) number of G's = 21,608,747 bp (22.2%) number of N's = 24,026 bp (0.02%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 839,968 number of insertions = 6,888 mapped reads with insertion percentage = 0.45% number of deletions = 26,231 mapped reads with deletion percentage = 1.7% homopolymer indels = 48.31% >>>>>>> Coverage mean coverageData = 0.0315X std coverageData = 0.3225X There is a 2.05% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 7430049 0.02980955060489097 0.43722995753587995 chr2 243199373 10351937 0.04256564016717263 0.400001835950193 chr3 198022430 6665453 0.03366009093010322 0.26246034896845805 chr4 191154276 6544748 0.03423804131904431 0.2722439387752692 chr5 180915260 5483664 0.03031067694344855 0.25003303206600386 chr6 171115067 5192700 0.03034624648219902 0.2714680173845649 chr7 159138663 5479343 0.03443124943182412 0.3776951177897525 chr8 146364022 5254385 0.03589943025752599 0.5129615145125186 chr9 141213431 3886614 0.027522976904371086 0.3076757451645555 chr10 135534747 4557899 0.03362900732754531 0.2991052640066673 chr11 135006516 4383267 0.03246707736684354 0.30732357484107287 chr12 133851895 4848829 0.03622532949570867 0.2727758477734315 chr13 115169878 2570107 0.022315791634336887 0.21467230736685897 chr14 107349540 3223178 0.030025075095803856 0.2565973468185268 chr15 102531392 2785901 0.02717120040660328 0.23980266586752014 chr16 90354753 2735570 0.030275883771161437 0.2514266855392297 chr17 81195210 2193695 0.027017542044660024 0.24323188499630286 chr18 78077248 2198964 0.028163953729516696 0.457045784002242 chr19 59128983 1655073 0.027990892385211495 0.3567814607661571 chr20 63025520 1951629 0.03096569453135809 0.25101229550196613 chr21 48129895 1378062 0.028632142247557366 0.2461990640330967 chr22 51304566 868054 0.016919624658748696 0.17938966074712476 chrMT 16571 21245 1.2820590187677268 1.6965405264236393 chrX 155270560 5486840 0.03533728480144594 0.2815727632513743 chrY 59373566 225194 0.003792832655528893 0.09262325385068292