BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716551.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 = 1,855,029 number of mapped reads = 1,636,368 (88.21%) number of supplementary alignments = 6,202 (0.33%) number of secondary alignments = 0 number of mapped bases = 92,711,355 bp number of sequenced bases = 92,683,854 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,126 duplication rate = 1.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2131 >>>>>>> ACTG content number of A's = 24,030,569 bp (25.93%) number of C's = 17,949,770 bp (19.37%) number of T's = 27,843,679 bp (30.04%) number of G's = 22,859,186 bp (24.66%) number of N's = 650 bp (0%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 485,179 number of insertions = 7,427 mapped reads with insertion percentage = 0.45% number of deletions = 17,391 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.32% >>>>>>> Coverage mean coverageData = 0.0299X std coverageData = 0.2499X There is a 2.7% of reference with a coverageData >= 1X There is a 0.21% 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% 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 7834116 0.031430677960076175 0.3129287840227759 chr2 243199373 7252502 0.029821219974938012 0.3786299042753837 chr3 198022430 5407215 0.027306073357447436 0.18271947964297514 chr4 191154276 5705401 0.02984710109231352 0.19868881212463166 chr5 180915260 5334994 0.029488910996231053 0.1857396942999731 chr6 171115067 5008428 0.029269357092908715 0.22241716279061277 chr7 159138663 5295134 0.03327371174407818 0.3513565431202595 chr8 146364022 4844443 0.033098591674393864 0.24798315341476923 chr9 141213431 3081689 0.021822917113316225 0.18839663954783797 chr10 135534747 4085525 0.030143746090439818 0.3049021653552699 chr11 135006516 3307530 0.02449903973523767 0.20846674063469653 chr12 133851895 4663151 0.03483813957209945 0.20494171996173446 chr13 115169878 2841913 0.024675835811860457 0.17061883306928496 chr14 107349540 3119974 0.029063692308322887 0.1941857904275345 chr15 102531392 3452926 0.033676768964572334 0.20716886624545813 chr16 90354753 3206850 0.03549176876173852 0.21779508297293976 chr17 81195210 4159506 0.0512284653244939 0.2601926992804798 chr18 78077248 1738430 0.022265513251696577 0.28959936195667824 chr19 59128983 2355715 0.03984027596077545 0.30465082147615036 chr20 63025520 2663479 0.042260325658558626 0.23209544773147417 chr21 48129895 1138133 0.02364711163404782 0.17771786876015783 chr22 51304566 837261 0.016319424668751706 0.1394138408947956 chrMT 16571 1764 0.10645102890591998 0.41092881842856444 chrX 155270560 5099319 0.03284150582054963 0.21091931168584305 chrY 59373566 275957 0.00464780909403353 0.12087531512357193