BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716436.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 = 983,718 number of mapped reads = 907,924 (92.3%) number of supplementary alignments = 3,196 (0.32%) number of secondary alignments = 0 number of mapped bases = 52,939,870 bp number of sequenced bases = 52,922,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,474 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5243 >>>>>>> ACTG content number of A's = 13,432,451 bp (25.38%) number of C's = 10,769,128 bp (20.35%) number of T's = 16,209,828 bp (30.63%) number of G's = 12,509,636 bp (23.64%) number of N's = 1,100 bp (0%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 264,750 number of insertions = 3,303 mapped reads with insertion percentage = 0.36% number of deletions = 10,979 mapped reads with deletion percentage = 1.2% homopolymer indels = 44.82% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.183X There is a 1.6% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4500796 0.01805731107887591 0.27476063809817314 chr2 243199373 4213894 0.017326911447259365 0.2534568149063778 chr3 198022430 3033912 0.015321052266654842 0.1307104366688544 chr4 191154276 3215109 0.016819445880457314 0.1518617343965153 chr5 180915260 3026369 0.016728102427622744 0.1356711308851366 chr6 171115067 2832049 0.016550553084843194 0.1515630781744752 chr7 159138663 3004335 0.01887872465033843 0.23107332099368252 chr8 146364022 2817439 0.019249532511480177 0.22493489119133012 chr9 141213431 1770169 0.012535415275052697 0.13807349330859384 chr10 135534747 2383277 0.017584250922754147 0.189113563589998 chr11 135006516 1890027 0.01399952428962762 0.14358656461125138 chr12 133851895 2628123 0.019634559525660806 0.14801607438778963 chr13 115169878 1610330 0.013982215037164491 0.12458249020623768 chr14 107349540 1820724 0.016960706119467303 0.13857037519789892 chr15 102531392 1938153 0.01890302045250688 0.1441195149046531 chr16 90354753 1826681 0.020216767124580596 0.15420538766630743 chr17 81195210 2305779 0.028397968303795262 0.18139408064862694 chr18 78077248 1005921 0.012883663625029407 0.20307452424003092 chr19 59128983 1307087 0.0221056905375829 0.22551998155165712 chr20 63025520 1576719 0.025017151782325636 0.17047189041163713 chr21 48129895 691321 0.014363650699840505 0.14381077450252863 chr22 51304566 492459 0.009598736299611228 0.10287234994351091 chrMT 16571 4058 0.24488564359423087 0.5308794257787182 chrX 155270560 2852534 0.01837137703374033 0.14934522287357868 chrY 59373566 192605 0.003243952030774099 0.13699861598565033