BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716503.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 = 878,343 number of mapped reads = 801,909 (91.3%) number of supplementary alignments = 3,138 (0.36%) number of secondary alignments = 0 number of mapped bases = 46,248,639 bp number of sequenced bases = 46,234,467 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,508 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1107 >>>>>>> ACTG content number of A's = 11,042,423 bp (23.88%) number of C's = 9,396,358 bp (20.32%) number of T's = 14,840,156 bp (32.1%) number of G's = 10,954,194 bp (23.69%) number of N's = 1,336 bp (0%) GC percentage = 44.02% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 236,371 number of insertions = 3,333 mapped reads with insertion percentage = 0.41% number of deletions = 9,009 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.38% >>>>>>> Coverage mean coverageData = 0.0149X std coverageData = 0.1655X There is a 1.39% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 3735916 0.014988592545974037 0.27770615961345574 chr2 243199373 3908798 0.016072401634028885 0.2074063359312133 chr3 198022430 3092559 0.015617215686122022 0.1323796862729824 chr4 191154276 2974431 0.015560368631251544 0.1379514011533876 chr5 180915260 2766635 0.015292435806686511 0.1309563057447389 chr6 171115067 2689972 0.015720252150560183 0.1450971038409043 chr7 159138663 2562887 0.016104741309784662 0.18573613044510806 chr8 146364022 2345217 0.016023179521535695 0.15861057640163412 chr9 141213431 1935025 0.013702839639948979 0.14756423070683072 chr10 135534747 2175044 0.016047869997499607 0.15980693305576543 chr11 135006516 2084341 0.015438817782691319 0.14936326575816314 chr12 133851895 2042985 0.015263026347142862 0.1320383717827183 chr13 115169878 1426867 0.012389237748432798 0.11755904902020393 chr14 107349540 1382590 0.012879328593303707 0.12216127950930775 chr15 102531392 1332974 0.01300064276899703 0.12111516543549601 chr16 90354753 1366680 0.015125712313108752 0.13537389323968493 chr17 81195210 1276790 0.01572494239500089 0.13715669646054487 chr18 78077248 1254039 0.016061516410004615 0.21721535234004521 chr19 59128983 988653 0.016720277431458614 0.20990401220766686 chr20 63025520 972671 0.015432970644272351 0.13325602065070818 chr21 48129895 614313 0.012763647209286452 0.12615581132826625 chr22 51304566 576695 0.011240617453035272 0.1124364950153169 chrMT 16571 4392 0.265041337275964 0.551574489363776 chrX 155270560 2591130 0.016687838312684646 0.14323107266212778 chrY 59373566 147035 0.0024764387572745756 0.07358970793765023