BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716638.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,955,337 number of mapped reads = 1,780,068 (91.04%) number of supplementary alignments = 5,583 (0.29%) number of secondary alignments = 0 number of mapped bases = 101,954,009 bp number of sequenced bases = 101,922,691 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,324 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5132 >>>>>>> ACTG content number of A's = 25,249,757 bp (24.77%) number of C's = 19,668,113 bp (19.3%) number of T's = 32,272,834 bp (31.66%) number of G's = 24,730,014 bp (24.26%) number of N's = 1,973 bp (0%) GC percentage = 43.56% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 530,269 number of insertions = 8,190 mapped reads with insertion percentage = 0.46% number of deletions = 19,598 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.92% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.3188X There is a 2.96% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 8627985 0.03461570111795228 0.5260372610814351 chr2 243199373 8073536 0.033197190849665555 0.46446807351792035 chr3 198022430 5867615 0.029631062501354014 0.1972291977139785 chr4 191154276 6339373 0.03316364735675596 0.22954467221733302 chr5 180915260 5856297 0.03237038710830695 0.19756743043367403 chr6 171115067 5517242 0.03224287666030017 0.24999511691727835 chr7 159138663 5886669 0.03699081599045481 0.4640689730736695 chr8 146364022 5346833 0.03653106089145323 0.3634603153039582 chr9 141213431 3417874 0.024203604259144442 0.22377953000233816 chr10 135534747 4539060 0.03349000976111314 0.35552961000234784 chr11 135006516 3641313 0.026971387069939647 0.24584799290456316 chr12 133851895 5129320 0.038320862024403914 0.21797332282071813 chr13 115169878 3115943 0.02705519059419339 0.18052617952286504 chr14 107349540 3438984 0.03203538645810685 0.20507244217529055 chr15 102531392 3762974 0.036700701381290134 0.21656825132340718 chr16 90354753 3534130 0.039113935710720166 0.23831380523052317 chr17 81195210 4498429 0.05540264013111118 0.27105721234258234 chr18 78077248 1929429 0.024711795682142896 0.3803413611333603 chr19 59128983 2485651 0.042037776973096255 0.41861100996343853 chr20 63025520 2696672 0.04278698533546411 0.2380844753456777 chr21 48129895 1310392 0.027226155386376804 0.20548144710404065 chr22 51304566 941084 0.018343084707119442 0.1493999084754389 chrMT 16571 109549 6.610886488443667 4.725965966680443 chrX 155270560 5526658 0.03559372749090362 0.23517382912384852 chrY 59373566 360997 0.006080096317610433 0.22094989489558867