BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238281.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 = 1,152,324 number of mapped reads = 912,770 (79.21%) number of supplementary alignments = 11,277 (0.98%) number of secondary alignments = 0 number of mapped bases = 59,108,420 bp number of sequenced bases = 59,072,133 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,628 duplication rate = 7.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3531 >>>>>>> ACTG content number of A's = 16,470,879 bp (27.88%) number of C's = 11,553,188 bp (19.56%) number of T's = 17,946,645 bp (30.38%) number of G's = 13,089,493 bp (22.16%) number of N's = 11,928 bp (0.02%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 562,894 number of insertions = 4,732 mapped reads with insertion percentage = 0.51% number of deletions = 21,754 mapped reads with deletion percentage = 2.35% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.0191X std coverageData = 0.231X There is a 1.26% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 4524501 0.01815241615787188 0.2878097643918614 chr2 243199373 5275548 0.02169227632013673 0.26932751661473264 chr3 198022430 4332765 0.02188017286728579 0.21180049127673878 chr4 191154276 3782446 0.019787399367409392 0.20653186400048454 chr5 180915260 3915325 0.02164176200504037 0.20873724179607558 chr6 171115067 3446902 0.020143766767189472 0.21581299225637812 chr7 159138663 3505229 0.02202625643524478 0.29148325234302946 chr8 146364022 2916274 0.019924800918630126 0.27560750500795694 chr9 141213431 2233535 0.01581673205008382 0.2009949620081338 chr10 135534747 2695898 0.019890825486987482 0.2269801373486002 chr11 135006516 2613456 0.01935799898724888 0.21658326012426293 chr12 133851895 2553978 0.019080626389338756 0.19737248331697554 chr13 115169878 2054433 0.017838284069381406 0.1954360596663728 chr14 107349540 1948729 0.018153119240194228 0.2324661671049642 chr15 102531392 1621522 0.015814883309104005 0.21258306616687175 chr16 90354753 1727906 0.019123576155423722 0.20132137799778158 chr17 81195210 1560848 0.019223400001059175 0.20395630342947463 chr18 78077248 1505136 0.019277523715999827 0.3024149447923051 chr19 59128983 1114163 0.018842925135377348 0.24643430483524428 chr20 63025520 1176686 0.018669992726755767 0.1951702255641886 chr21 48129895 768767 0.015972754563457908 0.18580113037531124 chr22 51304566 655873 0.012783910890114537 0.16173835275997692 chrMT 16571 12431 0.7501659525677388 1.423701470365803 chrX 155270560 2879901 0.018547630664821457 0.2019983084941926 chrY 59373566 286168 0.004819787984437384 0.11326043357238005