BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008800.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 = 1,588,055 number of mapped reads = 1,413,922 (89.03%) number of supplementary alignments = 10,004 (0.63%) number of secondary alignments = 0 number of mapped bases = 93,020,215 bp number of sequenced bases = 92,973,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,917 duplication rate = 4.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0427 >>>>>>> ACTG content number of A's = 25,091,598 bp (26.99%) number of C's = 18,202,283 bp (19.58%) number of T's = 28,342,141 bp (30.48%) number of G's = 21,211,557 bp (22.81%) number of N's = 125,887 bp (0.14%) GC percentage = 42.39% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 795,144 number of insertions = 6,919 mapped reads with insertion percentage = 0.48% number of deletions = 26,253 mapped reads with deletion percentage = 1.84% homopolymer indels = 44.95% >>>>>>> Coverage mean coverageData = 0.03X std coverageData = 0.3441X There is a 2.3% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9161464 0.03675603279640374 0.5963221480984986 chr2 243199373 6492733 0.026697161756251732 0.3731442006158665 chr3 198022430 7473574 0.03774104781968386 0.2717917866448808 chr4 191154276 4170957 0.021819846708529815 0.1911177269659767 chr5 180915260 4682123 0.025880199381743695 0.19971387496959397 chr6 171115067 4845508 0.02831724923439968 0.2222305768023887 chr7 159138663 4548925 0.028584662672451886 0.41057552931819186 chr8 146364022 6465145 0.044171681753867084 0.33067324707993756 chr9 141213431 2882796 0.020414460434716016 0.21816731169647355 chr10 135534747 6930546 0.051134828178046474 0.7277536537656514 chr11 135006516 4153820 0.030767551989860992 0.256371790218948 chr12 133851895 3354765 0.02506326115143906 0.19796979705888615 chr13 115169878 2446797 0.021245112372177733 0.18059416086280783 chr14 107349540 2742127 0.025543910108976713 0.1991100075887049 chr15 102531392 3160354 0.030823281907652243 0.22000429014093667 chr16 90354753 2771941 0.030678419319014685 0.3354787471540658 chr17 81195210 2808195 0.03458572248289031 0.28987019792662044 chr18 78077248 1241059 0.01589527079642971 0.3281384779286974 chr19 59128983 3116380 0.052704779312710316 0.44826238282080755 chr20 63025520 1723158 0.02734063915696372 0.20968851740760253 chr21 48129895 769988 0.015998123411655064 0.16312439842032025 chr22 51304566 1664200 0.03243765866765153 0.22544887153767548 chrMT 16571 207858 12.543479572747572 7.916316232328103 chrX 155270560 4937082 0.031796639362928814 0.2397215074411106 chrY 59373566 268720 0.00452591983442598 0.1644848986552552