BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008685.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 = 1,372,473 number of mapped reads = 1,100,809 (80.21%) number of supplementary alignments = 8,655 (0.63%) number of secondary alignments = 0 number of mapped bases = 70,563,240 bp number of sequenced bases = 70,517,675 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,816 duplication rate = 3.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1654 >>>>>>> ACTG content number of A's = 19,224,778 bp (27.26%) number of C's = 12,703,867 bp (18.02%) number of T's = 22,677,099 bp (32.16%) number of G's = 15,889,629 bp (22.53%) number of N's = 22,302 bp (0.03%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 585,344 number of insertions = 4,300 mapped reads with insertion percentage = 0.39% number of deletions = 25,775 mapped reads with deletion percentage = 2.31% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.0228X std coverageData = 0.2127X There is a 1.93% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 3103024 0.012449413315604136 0.3020395466145932 chr2 243199373 7934566 0.03262576667909419 0.2612104898053823 chr3 198022430 5160987 0.02606263845969368 0.18545039930059626 chr4 191154276 2238883 0.011712440060718286 0.13015478009590137 chr5 180915260 4155886 0.02297145083283743 0.17362394027730932 chr6 171115067 4105020 0.02398982200673188 0.19974761391439827 chr7 159138663 3803420 0.02390003741579757 0.23137598419548303 chr8 146364022 8000016 0.05465835039706684 0.3118147617285046 chr9 141213431 2233702 0.01581791465714051 0.1622489652146821 chr10 135534747 3312525 0.024440411579474894 0.22341375798221674 chr11 135006516 3310765 0.024523001541644107 0.234553877643692 chr12 133851895 2392961 0.01787767741353232 0.15304202347944923 chr13 115169878 3530890 0.030658103154368194 0.20099270216000673 chr14 107349540 1499248 0.013966040282985842 0.13988560473086695 chr15 102531392 1114718 0.01087196787497043 0.11973410532260506 chr16 90354753 1669396 0.018476017526161573 0.1629037769587437 chr17 81195210 1298489 0.015992187223852244 0.15805394409970683 chr18 78077248 1402767 0.017966399123083846 0.24414493757411931 chr19 59128983 999809 0.016908949710838086 0.2307989032958048 chr20 63025520 1719164 0.027277268001914146 0.190479464279793 chr21 48129895 525331 0.010914858634119189 0.12581498998479657 chr22 51304566 263243 0.0051309858073840834 0.07991063372203104 chrMT 16571 9572 0.5776356285076338 0.881028574787593 chrX 155270560 6562406 0.04226432879484688 0.2512485312572044 chrY 59373566 216452 0.0036455954153065354 0.09615534111044047