BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174054.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,160,804 number of mapped reads = 5,047,330 (97.8%) number of supplementary alignments = 558,200 (10.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,518,242 number of mapped paired reads (second in pair) = 2,529,088 number of mapped paired reads (both in pair) = 4,970,242 number of mapped paired reads (singletons) = 77,088 number of mapped bases = 601,442,926 bp number of sequenced bases = 601,149,825 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,033,729 duplication rate = 66.13% >>>>>>> Insert size mean insert size = 1,119,215.0769 std insert size = 9,859,992.7931 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 52.672 >>>>>>> ACTG content number of A's = 181,829,016 bp (30.25%) number of C's = 116,529,065 bp (19.38%) number of T's = 182,050,415 bp (30.28%) number of G's = 120,733,758 bp (20.08%) number of N's = 7,571 bp (0%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 5,882,456 number of insertions = 62,321 mapped reads with insertion percentage = 1.19% number of deletions = 109,438 mapped reads with deletion percentage = 2.11% homopolymer indels = 44.5% >>>>>>> Coverage mean coverageData = 0.1943X std coverageData = 2.8486X There is a 3.94% of reference with a coverageData >= 1X There is a 3.12% of reference with a coverageData >= 2X There is a 2.45% of reference with a coverageData >= 3X There is a 2.03% of reference with a coverageData >= 4X There is a 1.57% of reference with a coverageData >= 5X There is a 1.28% of reference with a coverageData >= 6X There is a 0.96% of reference with a coverageData >= 7X There is a 0.78% of reference with a coverageData >= 8X There is a 0.57% of reference with a coverageData >= 9X There is a 0.48% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 51686366 0.20736705005039888 2.064040339594014 chr2 243199373 64899385 0.2668567118386444 8.370328946290082 chr3 198022430 40458151 0.2043109510372133 1.3305760617064388 chr4 191154276 41306504 0.21608987705825633 1.5477151588519387 chr5 180915260 38655370 0.2136656133927011 1.3534364700112747 chr6 171115067 35211097 0.20577438104851398 1.3994783622175817 chr7 159138663 40729623 0.25593794890685995 2.6588488743867744 chr8 146364022 26077855 0.17817121068181632 1.607846269363085 chr9 141213431 20201508 0.143056562374722 1.423403139470378 chr10 135534747 22128749 0.16326993254357128 2.653202921254298 chr11 135006516 30235012 0.22395224242361753 1.4112374384471444 chr12 133851895 28397019 0.2121525362042876 1.3567389994269765 chr13 115169878 18283839 0.15875539088441162 1.1749474239053694 chr14 107349540 15580243 0.14513562889976053 1.1160133238170757 chr15 102531392 17868232 0.17427084185104988 1.2070097034548888 chr16 90354753 24780354 0.27425623088140144 2.211697519801449 chr17 81195210 13402008 0.16505909646640485 1.4068628976568376 chr18 78077248 10578977 0.13549372283203423 1.8316575764495089 chr19 59128983 11023034 0.1864235344619406 2.3968297868586985 chr20 63025520 14747235 0.23398831140147675 1.4115514166982472 chr21 48129895 9513578 0.19766463234544768 1.3405621540391701 chr22 51304566 5073100 0.09888203712706585 0.8675250065549315 chrMT 16571 1341548 80.95757648904713 76.50526414066617 chrX 155270560 18494366 0.1191105770469302 1.0136174155805042 chrY 59373566 769773 0.012964911017808835 0.5197483035035028