BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240237.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 = 3,328,611 number of mapped reads = 2,744,709 (82.46%) number of supplementary alignments = 20,031 (0.6%) number of secondary alignments = 0 number of mapped bases = 180,599,186 bp number of sequenced bases = 180,510,995 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 577,163 duplication rate = 14.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8466 >>>>>>> ACTG content number of A's = 49,944,266 bp (27.67%) number of C's = 32,817,922 bp (18.18%) number of T's = 58,333,154 bp (32.32%) number of G's = 39,347,729 bp (21.8%) number of N's = 67,924 bp (0.04%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,584,559 number of insertions = 13,255 mapped reads with insertion percentage = 0.48% number of deletions = 50,519 mapped reads with deletion percentage = 1.82% homopolymer indels = 48.99% >>>>>>> Coverage mean coverageData = 0.0583X std coverageData = 0.6603X There is a 1.96% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 14506039 0.058198607256428864 0.9133461718144472 chr2 243199373 20061167 0.08248856381714438 0.7896528389555983 chr3 198022430 11493677 0.0580422985416349 0.5580462724838692 chr4 191154276 11899935 0.0622530410985941 0.5758635831880908 chr5 180915260 9066032 0.050112035878012724 0.5164227921960072 chr6 171115067 9292480 0.054305445820267834 0.577912270490032 chr7 159138663 10515255 0.06607605469200153 0.8691948657813212 chr8 146364022 10150261 0.06934942659610707 0.890035089601971 chr9 141213431 6688496 0.04736444651642237 0.5971850264194593 chr10 135534747 8571103 0.06323915593393921 0.6307370071926339 chr11 135006516 7870050 0.058293853016694396 0.6395647909615837 chr12 133851895 9263579 0.06920767912923459 0.6042256230630066 chr13 115169878 4636499 0.04025791361869811 0.4676801756192936 chr14 107349540 5988336 0.05578352734441153 0.5473171939454871 chr15 102531392 5235696 0.051064321842036436 0.5165676189907946 chr16 90354753 5320388 0.05888332183255484 0.5505283878529802 chr17 81195210 4239213 0.05221013653391623 0.5346916925263276 chr18 78077248 4251958 0.05445834873688171 0.8270318238750739 chr19 59128983 3201976 0.05415239426661541 0.6803797973084865 chr20 63025520 3805746 0.0603842062707297 0.5686018753996094 chr21 48129895 2871468 0.05966079917689411 0.5611949358740957 chr22 51304566 1450025 0.028263078962601496 0.3578268105949764 chrMT 16571 43379 2.617765976706294 3.5746982953070745 chrX 155270560 9741962 0.06274184880894357 0.5919882898581931 chrY 59373566 434466 0.007317498834413954 0.16409232121592002