BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716451.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 = 1,315,162 number of mapped reads = 1,224,498 (93.11%) number of supplementary alignments = 19,539 (1.49%) number of secondary alignments = 0 number of mapped bases = 96,733,413 bp number of sequenced bases = 96,692,659 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,595 duplication rate = 2.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9612 >>>>>>> ACTG content number of A's = 24,131,017 bp (24.96%) number of C's = 19,123,481 bp (19.78%) number of T's = 29,734,665 bp (30.75%) number of G's = 23,697,795 bp (24.51%) number of N's = 5,701 bp (0.01%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 763,985 number of insertions = 8,563 mapped reads with insertion percentage = 0.69% number of deletions = 23,165 mapped reads with deletion percentage = 1.86% homopolymer indels = 44.34% >>>>>>> Coverage mean coverageData = 0.0312X std coverageData = 0.3494X There is a 2.75% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% 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 7724850 0.030992299914871627 0.5231720228999575 chr2 243199373 8241139 0.033886349698771634 0.49138836777418926 chr3 198022430 6350330 0.03206874089970515 0.20055375847148293 chr4 191154276 6263169 0.032764995536903395 0.21910639671680882 chr5 180915260 5893552 0.03257631224696026 0.20494840961868485 chr6 171115067 5533291 0.032336667349111926 0.2365133700289468 chr7 159138663 5396158 0.03390852919255706 0.462502045280558 chr8 146364022 4962955 0.03390829885776164 0.44522404110464137 chr9 141213431 4143688 0.02934344113485919 0.4051620370279681 chr10 135534747 4592964 0.033887723271435334 0.37076383584309514 chr11 135006516 4437335 0.032867561740501476 0.33866306244693284 chr12 133851895 4401880 0.03288619858538424 0.20521593504594077 chr13 115169878 3012748 0.0261591663750829 0.17645160097238147 chr14 107349540 2879471 0.02682331941059086 0.24347308334132384 chr15 102531392 2739710 0.02672069447764837 0.18189896218982549 chr16 90354753 2796947 0.03095517288393229 0.22178196592004565 chr17 81195210 2683262 0.03304704797241118 0.21773309147187694 chr18 78077248 2625732 0.03362992507112956 0.7247445745426526 chr19 59128983 2095424 0.035438187732740135 0.4074151836200895 chr20 63025520 1932430 0.030661071895955797 0.20346028837005578 chr21 48129895 1232671 0.02561133781821049 0.1879761956875679 chr22 51304566 1077373 0.020999553918846132 0.15942733034503906 chrMT 16571 2608 0.1573833806046708 0.44959191651943087 chrX 155270560 5453342 0.03512154525622887 0.2722845696435608 chrY 59373566 260384 0.004385520654090408 0.127882939696261