BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082921.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,841,559 number of mapped reads = 1,677,173 (91.07%) number of supplementary alignments = 19,456 (1.06%) number of secondary alignments = 0 number of mapped bases = 113,012,796 bp number of sequenced bases = 112,968,425 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,474 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1042 >>>>>>> ACTG content number of A's = 31,328,590 bp (27.73%) number of C's = 20,977,068 bp (18.57%) number of T's = 35,858,522 bp (31.74%) number of G's = 24,799,020 bp (21.95%) number of N's = 5,225 bp (0%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 815,912 number of insertions = 9,234 mapped reads with insertion percentage = 0.55% number of deletions = 26,764 mapped reads with deletion percentage = 1.58% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.0365X std coverageData = 0.2898X There is a 3.03% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10915634 0.04379380864210565 0.47072813487519377 chr2 243199373 10473880 0.04306705182171666 0.372649122258682 chr3 198022430 7476759 0.03775713185622457 0.22578635508463138 chr4 191154276 7192637 0.0376273926511589 0.2310082739200948 chr5 180915260 6472242 0.035774992115093 0.22062762177778503 chr6 171115067 8829509 0.05159983369553307 0.3202354858772048 chr7 159138663 7724704 0.04854071194502872 0.33447660107287486 chr8 146364022 7561794 0.051664294931714844 0.33304392681414446 chr9 141213431 2947881 0.020875358520252935 0.227384604460914 chr10 135534747 3599573 0.026558303901212874 0.20358760481737748 chr11 135006516 4779326 0.03540070614073176 0.2504901841246119 chr12 133851895 4491990 0.03355940534125423 0.21378190870136468 chr13 115169878 3140260 0.027266330871688515 0.19334744719891886 chr14 107349540 2311417 0.021531689842359827 0.17866458043316646 chr15 102531392 1572202 0.015333859897269316 0.14885469661895226 chr16 90354753 2992625 0.0331208364877053 0.22129443313348268 chr17 81195210 3204323 0.03946443392411941 0.2446144829069064 chr18 78077248 5185930 0.06642050191113294 0.5428787728578068 chr19 59128983 1914069 0.03237107934022813 0.29686910535511113 chr20 63025520 1874757 0.029745998129011866 0.2082466546076288 chr21 48129895 2478595 0.051498034641463485 0.26957306061912895 chr22 51304566 1883063 0.036703614255308194 0.2230876999988429 chrMT 16571 6680 0.40311387363466294 0.6625772530309828 chrX 155270560 3792654 0.024426098546949274 0.19362364317945865 chrY 59373566 190292 0.0032049953004338666 0.07127477489109647