BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524346.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 = 1,836,118 number of mapped reads = 1,700,614 (92.62%) number of supplementary alignments = 7,736 (0.42%) number of secondary alignments = 0 number of mapped bases = 100,027,634 bp number of sequenced bases = 99,999,107 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,699 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7804 >>>>>>> ACTG content number of A's = 25,326,723 bp (25.33%) number of C's = 20,004,248 bp (20%) number of T's = 30,954,264 bp (30.95%) number of G's = 23,700,259 bp (23.7%) number of N's = 13,613 bp (0.01%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 507,718 number of insertions = 6,876 mapped reads with insertion percentage = 0.4% number of deletions = 18,138 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.56% >>>>>>> Coverage mean coverageData = 0.0323X std coverageData = 0.3044X There is a 2.86% of reference with a coverageData >= 1X There is a 0.26% 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 8634796 0.03464302702780427 0.5837217106934479 chr2 243199373 6569854 0.027014271948801447 0.37470223357736465 chr3 198022430 6994405 0.035321276483679144 0.20625263763043447 chr4 191154276 5004406 0.026179932276273014 0.21993438182698755 chr5 180915260 5525121 0.030539828425750266 0.19277441383938568 chr6 171115067 6478047 0.03785784100473163 0.22770142970656165 chr7 159138663 4598844 0.028898345086636804 0.3470833046837146 chr8 146364022 10479069 0.07159593496276018 0.40230747367248915 chr9 141213431 4137957 0.02930285717652452 0.23229733917702014 chr10 135534747 5210903 0.03844698953840966 0.3129008631692607 chr11 135006516 4900426 0.03629769988287084 0.2602777951662145 chr12 133851895 3846432 0.028736477731600287 0.18913518812050445 chr13 115169878 2476522 0.021503209372158924 0.16253337104407614 chr14 107349540 2098246 0.01954592446320683 0.16108428148292703 chr15 102531392 3133452 0.030560903727904133 0.19082250083726443 chr16 90354753 3232548 0.03577618102724491 0.21979509111504023 chr17 81195210 3161162 0.03893286315781436 0.23908917676065422 chr18 78077248 2331175 0.029857289539713287 0.4286890857411141 chr19 59128983 1801318 0.0304642141401282 0.3807131437537736 chr20 63025520 2237095 0.03549506612559484 0.21203643650405576 chr21 48129895 1388043 0.028839518557021576 0.2254189873623405 chr22 51304566 738335 0.014391214224480527 0.13091027650784517 chrMT 16571 5294 0.3194737794942973 0.5975381378318965 chrX 155270560 4727258 0.030445294974140624 0.21145377911749005 chrY 59373566 316926 0.005337829969653499 0.17849838499186232