BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238519.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 = 2,739,701 number of mapped reads = 2,314,323 (84.47%) number of supplementary alignments = 21,669 (0.79%) number of secondary alignments = 0 number of mapped bases = 138,647,736 bp number of sequenced bases = 138,571,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 941,036 duplication rate = 22.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.9316 >>>>>>> ACTG content number of A's = 33,076,581 bp (23.87%) number of C's = 23,713,836 bp (17.11%) number of T's = 48,181,065 bp (34.77%) number of G's = 33,597,090 bp (24.25%) number of N's = 2,909 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 930,047 number of insertions = 9,020 mapped reads with insertion percentage = 0.39% number of deletions = 46,881 mapped reads with deletion percentage = 2.01% homopolymer indels = 39.36% >>>>>>> Coverage mean coverageData = 0.0448X std coverageData = 1.1259X There is a 1.43% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 33087894 0.13274949473445846 1.144228072298923 chr2 243199373 3960364 0.01628443343067336 2.9190154022845234 chr3 198022430 2774992 0.014013523619521283 0.3163402818939168 chr4 191154276 2023887 0.010587715024486294 0.2176659551447454 chr5 180915260 8199841 0.04532420869306437 0.5735470715682912 chr6 171115067 14176375 0.08284702947870745 1.2105201161368446 chr7 159138663 12684719 0.07970859350502398 0.906046817993969 chr8 146364022 2439748 0.01666904179498429 0.5476177272372094 chr9 141213431 2970435 0.02103507420622051 0.4382296431948008 chr10 135534747 2877818 0.021233064315234234 0.3817013946538474 chr11 135006516 5667222 0.04197739611323649 0.5543721901171856 chr12 133851895 3540499 0.02645086944790733 0.4177670481167734 chr13 115169878 855473 0.0074279231241349405 0.6336530110965738 chr14 107349540 3122494 0.02908716702465609 0.44815841351865016 chr15 102531392 772293 0.007532258998297809 0.5945019381315366 chr16 90354753 5405094 0.05982080433555056 0.743367828205097 chr17 81195210 957183 0.011788663395291422 0.2606682529416082 chr18 78077248 3964766 0.050780042862166454 2.54260987449303 chr19 59128983 3229002 0.054609462841598344 0.7236004467207062 chr20 63025520 5926685 0.09403627292563393 0.8361631720151607 chr21 48129895 3993907 0.08298183488661257 0.8795416866278598 chr22 51304566 2450468 0.04776315620718827 0.5829219093917009 chrMT 16571 16682 1.0066984490978215 2.3420506500292464 chrX 155270560 13140708 0.084631033725904 0.7738013548291662 chrY 59373566 409187 0.006891736972645369 0.38873089926903037