BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238644.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 = 2,971,356 number of mapped reads = 2,494,822 (83.96%) number of supplementary alignments = 25,510 (0.86%) number of secondary alignments = 0 number of mapped bases = 151,053,114 bp number of sequenced bases = 150,953,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 626,597 duplication rate = 18.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0018 >>>>>>> ACTG content number of A's = 37,826,914 bp (25.06%) number of C's = 26,607,921 bp (17.63%) number of T's = 50,181,147 bp (33.24%) number of G's = 36,330,092 bp (24.07%) number of N's = 6,989 bp (0%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,024,758 number of insertions = 8,815 mapped reads with insertion percentage = 0.35% number of deletions = 59,179 mapped reads with deletion percentage = 2.34% homopolymer indels = 41.07% >>>>>>> Coverage mean coverageData = 0.0488X std coverageData = 0.6236X There is a 2.5% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 12271845 0.049234962588117284 0.43107508794336763 chr2 243199373 21610420 0.0888588639576797 1.5485526664670815 chr3 198022430 4757634 0.02402573284248658 0.2792256415216129 chr4 191154276 16791769 0.08784406685205409 0.5414702020804789 chr5 180915260 11171638 0.0617506671355418 0.4503374963764413 chr6 171115067 7974729 0.04660448164976612 0.6103983539867572 chr7 159138663 5816721 0.036551274783551496 0.3908926026227774 chr8 146364022 10554827 0.07211353484123305 0.7925824555786443 chr9 141213431 1391502 0.009853892722144823 0.2766733817053023 chr10 135534747 9659359 0.07126850651811081 0.4897180704037187 chr11 135006516 4780376 0.03540848354312025 0.3377715893026516 chr12 133851895 4132065 0.030870425853888734 0.32850771200588225 chr13 115169878 4496496 0.03904229194373202 0.4387236653292831 chr14 107349540 7527583 0.07012217285700525 0.5502208906027737 chr15 102531392 3356121 0.03273261909874393 0.561972689446929 chr16 90354753 986924 0.01092276794780237 0.20391657859819132 chr17 81195210 3680118 0.04532432393487251 0.4130215844029993 chr18 78077248 2172722 0.027827850694737602 0.7445798485483011 chr19 59128983 796885 0.013477062509260476 0.242552822933292 chr20 63025520 7925451 0.12574987084596842 0.6480599382961044 chr21 48129895 3015914 0.06266196923970019 0.45389747810638115 chr22 51304566 518901 0.010114129023136069 0.16639551174605993 chrMT 16571 30696 1.8523927342948525 2.439696830983236 chrX 155270560 5372803 0.034602844222369006 0.3505777903721872 chrY 59373566 259615 0.004372568762334403 0.20011721300206775