BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716104.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 = 1,198,483 number of mapped reads = 1,085,018 (90.53%) number of supplementary alignments = 5,392 (0.45%) number of secondary alignments = 0 number of mapped bases = 62,638,685 bp number of sequenced bases = 62,622,345 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,279 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4449 >>>>>>> ACTG content number of A's = 15,002,127 bp (23.96%) number of C's = 11,362,752 bp (18.14%) number of T's = 20,396,468 bp (32.57%) number of G's = 15,860,344 bp (25.33%) number of N's = 654 bp (0%) GC percentage = 43.47% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 314,577 number of insertions = 4,158 mapped reads with insertion percentage = 0.38% number of deletions = 10,547 mapped reads with deletion percentage = 0.97% homopolymer indels = 42.22% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.2256X There is a 1.86% of reference with a coverageData >= 1X There is a 0.11% 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 5824465 0.02336790567113572 0.2843954831968816 chr2 243199373 5860107 0.024095896826181372 0.2530713028873942 chr3 198022430 5410220 0.02732124840605178 0.18666861036906143 chr4 191154276 3373574 0.017648435968024068 0.14684344856793893 chr5 180915260 3232295 0.017866348034986105 0.1424552697047878 chr6 171115067 3386685 0.01979185737045587 0.15988923909361674 chr7 159138663 3042496 0.01911852181389761 0.49939533666509545 chr8 146364022 4311331 0.02945622114702478 0.24063127977039495 chr9 141213431 2929004 0.020741681433970684 0.16901421988559476 chr10 135534747 3100912 0.022879092399825707 0.3336855595842112 chr11 135006516 2158961 0.015991531845766616 0.1605640774336365 chr12 133851895 2777614 0.020751398401942685 0.17598730751635877 chr13 115169878 1621439 0.014078672550126344 0.12539132824315286 chr14 107349540 1871831 0.017436786408213768 0.1427921772606829 chr15 102531392 1399270 0.013647234985359412 0.12983733564975367 chr16 90354753 1826709 0.020217077014199794 0.161097147799531 chr17 81195210 2629539 0.032385395640949756 0.19942052828673923 chr18 78077248 1531487 0.01961502280408244 0.241288880299363 chr19 59128983 923489 0.015618212138030515 0.27675895798590566 chr20 63025520 1318101 0.02091376636003955 0.16417958415218917 chr21 48129895 624826 0.01298207693991437 0.1236118093084143 chr22 51304566 1191837 0.023230622397234585 0.16454469290704668 chrMT 16571 7585 0.4577273550178022 0.7788131207327755 chrX 155270560 2144578 0.013811877795765018 0.14431098786430957 chrY 59373566 140330 0.0023635097140703998 0.06467924840383563