BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004102.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 = 3,940,746 number of mapped reads = 3,499,915 (88.81%) number of supplementary alignments = 32,616 (0.83%) number of secondary alignments = 0 number of mapped bases = 229,621,044 bp number of sequenced bases = 229,521,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,455 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4092 >>>>>>> ACTG content number of A's = 66,384,567 bp (28.92%) number of C's = 43,715,253 bp (19.05%) number of T's = 70,669,912 bp (30.79%) number of G's = 48,703,147 bp (21.22%) number of N's = 48,443 bp (0.02%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 2,245,389 number of insertions = 21,488 mapped reads with insertion percentage = 0.61% number of deletions = 60,379 mapped reads with deletion percentage = 1.7% homopolymer indels = 45% >>>>>>> Coverage mean coverageData = 0.0742X std coverageData = 0.8503X There is a 6.23% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 17848767 0.0716097192792952 1.8528188634453069 chr2 243199373 19868299 0.08169551900941784 1.1264448750387375 chr3 198022430 15321980 0.07737497211805754 0.3408015199503832 chr4 191154276 15183373 0.07942994170844496 0.3916249196103471 chr5 180915260 13966318 0.0771981202691249 0.32269866317911555 chr6 171115067 12710445 0.07428010415938416 0.45304846957692235 chr7 159138663 13130016 0.08250676329987766 1.1257193614563517 chr8 146364022 13367593 0.09133114010764203 0.9948234955769224 chr9 141213431 9275284 0.06568273240241575 0.7619459861315447 chr10 135534747 10556504 0.07788780540535484 0.8234664806648642 chr11 135006516 10610277 0.07859085112603009 0.5650573674665063 chr12 133851895 9978530 0.07454903794974288 0.3268787633932808 chr13 115169878 7226302 0.0627447221920301 0.2865313579435899 chr14 107349540 6781872 0.06317560373337418 0.40417454687139936 chr15 102531392 6132275 0.05980875593691345 0.30230347392076623 chr16 90354753 5909321 0.0654013298005474 0.4010166310244296 chr17 81195210 5254488 0.06471426085356513 0.3587547019655906 chr18 78077248 7351071 0.09415125645821942 1.5298355693741699 chr19 59128983 4464280 0.0755007066500704 1.1197396095146053 chr20 63025520 5312240 0.08428712686543482 0.37772892821189247 chr21 48129895 3002763 0.06238872949961765 0.3613470295668388 chr22 51304566 2507403 0.048872901487949434 0.25020153484283525 chrMT 16571 522902 31.55524711845996 19.110639815357548 chrX 155270560 12645883 0.08144417718336303 0.4085040661351864 chrY 59373566 692858 0.01166946920452782 0.2728709936396754