BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716841.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 = 506,084 number of mapped reads = 415,598 (82.12%) number of supplementary alignments = 6,037 (1.19%) number of secondary alignments = 0 number of mapped bases = 33,276,180 bp number of sequenced bases = 33,262,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,931 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5346 >>>>>>> ACTG content number of A's = 8,533,128 bp (25.65%) number of C's = 6,205,011 bp (18.65%) number of T's = 10,234,615 bp (30.77%) number of G's = 8,287,412 bp (24.92%) number of N's = 2,166 bp (0.01%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 269,097 number of insertions = 3,049 mapped reads with insertion percentage = 0.72% number of deletions = 8,166 mapped reads with deletion percentage = 1.93% homopolymer indels = 43.2% >>>>>>> Coverage mean coverageData = 0.0107X std coverageData = 0.1532X There is a 1.01% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2733793 0.010968048902072746 0.2259339609694245 chr2 243199373 2929465 0.012045528587773127 0.20079794914252147 chr3 198022430 2197065 0.011095031002296052 0.10895078829024758 chr4 191154276 2210237 0.01156258204760222 0.11563362368105548 chr5 180915260 2046895 0.011314109158066599 0.1111256331877779 chr6 171115067 1981644 0.011580768629801607 0.11974364368371775 chr7 159138663 1896912 0.011919868900746011 0.18418651365397398 chr8 146364022 1728037 0.01180643286777129 0.19683781514251264 chr9 141213431 1460797 0.010344603835877339 0.16181734541362527 chr10 135534747 1613982 0.011908252575260276 0.14756663115860724 chr11 135006516 1536791 0.011383087613341567 0.15075974148075538 chr12 133851895 1542706 0.011525469998015344 0.11267839017877 chr13 115169878 1038500 0.009017114700772714 0.09781719599012563 chr14 107349540 1005235 0.009364129552860683 0.11151128607467424 chr15 102531392 957576 0.009339344578487728 0.10112481593980639 chr16 90354753 997932 0.01104459883809322 0.11860315733154866 chr17 81195210 919863 0.011329030370141293 0.11603825456446858 chr18 78077248 963957 0.012346195911003421 0.29233681331144845 chr19 59128983 696942 0.011786808509796288 0.17625450407903465 chr20 63025520 692987 0.010995339665583085 0.11363510882259015 chr21 48129895 605712 0.012584943308104038 0.11872004157916524 chr22 51304566 365379 0.007121763782194357 0.08743042126048917 chrMT 16571 9892 0.5969464727536057 0.8896703985020604 chrX 155270560 1065267 0.00686071461325315 0.10215953073191836 chrY 59373566 78614 0.001324057241230887 0.05280799408105979