BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524727.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 = 1,558,702 number of mapped reads = 1,417,856 (90.96%) number of supplementary alignments = 5,152 (0.33%) number of secondary alignments = 0 number of mapped bases = 80,653,651 bp number of sequenced bases = 80,627,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,136 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5369 >>>>>>> ACTG content number of A's = 18,729,592 bp (23.23%) number of C's = 14,007,749 bp (17.37%) number of T's = 27,039,451 bp (33.54%) number of G's = 20,839,871 bp (25.85%) number of N's = 10,509 bp (0.01%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 413,688 number of insertions = 5,815 mapped reads with insertion percentage = 0.41% number of deletions = 16,373 mapped reads with deletion percentage = 1.15% homopolymer indels = 43.1% >>>>>>> Coverage mean coverageData = 0.0261X std coverageData = 0.2379X There is a 2.33% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6418807 0.025752421294870115 0.3294094455040005 chr2 243199373 6827516 0.028073740140769195 0.3672284393078153 chr3 198022430 5250938 0.026516884981160973 0.18082646992515886 chr4 191154276 5261111 0.02752285279770566 0.2082487133554221 chr5 180915260 4856096 0.0268418263887745 0.1795743253026893 chr6 171115067 4554715 0.02661784891215921 0.19412438805139975 chr7 159138663 4468670 0.02808035404947445 0.28598467504074493 chr8 146364022 4086641 0.02792107612347521 0.22101054824942667 chr9 141213431 3435514 0.024328521555431932 0.20525619172188694 chr10 135534747 3938580 0.029059559169723467 0.28492991750214797 chr11 135006516 3614595 0.026773485510877118 0.21313645117033395 chr12 133851895 3627509 0.027100916277651505 0.18235156723321652 chr13 115169878 2499359 0.02170149906731689 0.16235154225474244 chr14 107349540 2392754 0.022289373573468503 0.1701394872334275 chr15 102531392 2318723 0.02261476173072926 0.16576048933434387 chr16 90354753 2405498 0.02662281640015108 0.1965291896490168 chr17 81195210 2307707 0.028421713546895194 0.19287849809394134 chr18 78077248 2102587 0.02692957364480879 0.31912389815156983 chr19 59128983 1716148 0.02902380377487636 0.27726813830958835 chr20 63025520 1736817 0.02755736089127071 0.18811776955590126 chr21 48129895 1058286 0.02198812193544158 0.18469697459517956 chr22 51304566 994277 0.019379893009912608 0.15439004823245656 chrMT 16571 25018 1.509745941705389 1.5940197080481964 chrX 155270560 4470880 0.0287941255573497 0.2028962825902635 chrY 59373566 284905 0.004798515891735389 0.13544805662753756