BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004035.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 = 468,757 number of mapped reads = 386,345 (82.42%) number of supplementary alignments = 3,445 (0.73%) number of secondary alignments = 0 number of mapped bases = 26,108,562 bp number of sequenced bases = 26,096,868 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,352 duplication rate = 1.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0174 >>>>>>> ACTG content number of A's = 7,729,402 bp (29.62%) number of C's = 4,616,805 bp (17.69%) number of T's = 7,995,819 bp (30.64%) number of G's = 5,749,430 bp (22.03%) number of N's = 5,412 bp (0.02%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 242,566 number of insertions = 2,268 mapped reads with insertion percentage = 0.58% number of deletions = 6,809 mapped reads with deletion percentage = 1.74% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 0.0084X std coverageData = 0.1204X There is a 0.81% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 1842439 0.0073919133786230365 0.17313974916440478 chr2 243199373 2116137 0.008701243649999049 0.11274408545520749 chr3 198022430 2012400 0.010162485128578615 0.10296013527345999 chr4 191154276 1629083 0.00852234663063462 0.09608458440193417 chr5 180915260 1579914 0.008732895168710479 0.09531652420449095 chr6 171115067 1541863 0.009010679345963146 0.09949139136474293 chr7 159138663 1524892 0.009582159176491259 0.13782826692047945 chr8 146364022 1598949 0.010924467489694974 0.22197779782608715 chr9 141213431 1085563 0.007687392001685732 0.10497284149834182 chr10 135534747 1199052 0.008846823611955391 0.10913674809806403 chr11 135006516 1149142 0.008511752129060201 0.11212270299883086 chr12 133851895 1214897 0.009076427345313266 0.09784118746830574 chr13 115169878 938418 0.008148120118699788 0.09234726402523893 chr14 107349540 723663 0.0067411839864427925 0.08653184311273299 chr15 102531392 698895 0.006816400190880077 0.08419228425097579 chr16 90354753 676189 0.007483712561308202 0.09323700820117298 chr17 81195210 625836 0.007707794585419509 0.09302463235332134 chr18 78077248 720585 0.009229129079959375 0.18367359250036136 chr19 59128983 437581 0.007400448609102579 0.12640239207908205 chr20 63025520 494036 0.00783866598799978 0.09131819507670609 chr21 48129895 311862 0.006479590283751917 0.0844255934450448 chr22 51304566 276436 0.0053881364087555094 0.07475396518092994 chrMT 16571 22020 1.32882746967594 1.4844515429166814 chrX 155270560 1621490 0.010442997049794888 0.1084432270785304 chrY 59373566 67220 0.0011321536590879516 0.03729371632497734