BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013242.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 = 1,962,442 number of mapped reads = 1,683,983 (85.81%) number of supplementary alignments = 23,011 (1.17%) number of secondary alignments = 0 number of mapped bases = 107,585,698 bp number of sequenced bases = 107,495,761 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 169,623 duplication rate = 8.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0328 >>>>>>> ACTG content number of A's = 30,272,509 bp (28.16%) number of C's = 18,911,204 bp (17.59%) number of T's = 35,205,044 bp (32.75%) number of G's = 23,084,958 bp (21.48%) number of N's = 22,046 bp (0.02%) GC percentage = 39.07% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,040,239 number of insertions = 7,679 mapped reads with insertion percentage = 0.45% number of deletions = 51,660 mapped reads with deletion percentage = 3.01% homopolymer indels = 42.92% >>>>>>> Coverage mean coverageData = 0.0348X std coverageData = 0.3645X There is a 2.25% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 6360192 0.025517256384288006 0.5395744517322952 chr2 243199373 11843398 0.048698308116115085 0.4280880964224526 chr3 198022430 8036749 0.04058504382559087 0.28897700530744497 chr4 191154276 6611759 0.034588601094123574 0.27347006245893823 chr5 180915260 3180287 0.017578876430877084 0.1893223227994012 chr6 171115067 6576632 0.03843397378911116 0.40366637962029933 chr7 159138663 7692654 0.04833931525489818 0.4966770782182633 chr8 146364022 7831254 0.053505321136911636 0.571526015567668 chr9 141213431 2253227 0.015956180542061896 0.2506869712561041 chr10 135534747 2521238 0.018602152258416802 0.2864862306397116 chr11 135006516 4884002 0.03617604649541508 0.3015640477617254 chr12 133851895 1662587 0.012421094225076156 0.15587828016988056 chr13 115169878 4184072 0.03632956874366056 0.275501689596245 chr14 107349540 4062706 0.03784558368857473 0.28475382849657327 chr15 102531392 4759766 0.046422523942716 0.30591848657598597 chr16 90354753 4367149 0.048333362164135404 0.32073839165771023 chr17 81195210 1894827 0.023336684516241782 0.2314674891246166 chr18 78077248 3269971 0.041881227678516535 0.532394162263649 chr19 59128983 1826247 0.030885817873782813 0.415188763277231 chr20 63025520 1545848 0.024527334324254683 0.22493350164898906 chr21 48129895 1628888 0.03384358100095585 0.2843977778230768 chr22 51304566 621004 0.01210426378034267 0.14967536527317224 chrMT 16571 9896 0.5971878583066803 1.0760981526551476 chrX 155270560 9599007 0.06182116558348215 0.37728051920145045 chrY 59373566 362338 0.006102682126251268 0.19969744173249174