BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063546.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 = 2,148,447 number of mapped reads = 1,950,527 (90.79%) number of supplementary alignments = 16,594 (0.77%) number of secondary alignments = 0 number of mapped bases = 129,607,451 bp number of sequenced bases = 129,548,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,397 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4977 >>>>>>> ACTG content number of A's = 36,018,613 bp (27.8%) number of C's = 23,593,947 bp (18.21%) number of T's = 41,549,537 bp (32.07%) number of G's = 28,382,584 bp (21.91%) number of N's = 3,420 bp (0%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,054,846 number of insertions = 10,130 mapped reads with insertion percentage = 0.51% number of deletions = 36,216 mapped reads with deletion percentage = 1.83% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.0419X std coverageData = 0.444X There is a 3.37% of reference with a coverageData >= 1X There is a 0.58% 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 10735038 0.043069252774299 0.9171314184587154 chr2 243199373 14411008 0.05925594224291031 0.5486478701246049 chr3 198022430 10095959 0.0509839163169546 0.27170422999030247 chr4 191154276 8643020 0.04521489228940921 0.2614478434746627 chr5 180915260 5189305 0.02868362237657564 0.20295923152034923 chr6 171115067 7523404 0.04396692899053711 0.28489704564166524 chr7 159138663 6584273 0.04137443959800014 0.48518925239274574 chr8 146364022 6568798 0.04487986808670781 0.7157134839719194 chr9 141213431 4688641 0.033202514568178715 0.4001675669126117 chr10 135534747 7225422 0.05331047690670791 0.3837868351193063 chr11 135006516 5973747 0.04424784208193329 0.3436832474236287 chr12 133851895 5678154 0.04242117005515686 0.260781530000105 chr13 115169878 3335771 0.02896391884690544 0.2048893687121951 chr14 107349540 2819589 0.026265496806041275 0.23450435468204753 chr15 102531392 2691410 0.026249619238564517 0.1987019911587524 chr16 90354753 3060828 0.03387567226264234 0.23845702005464348 chr17 81195210 4154024 0.05116094902642656 0.2942597958525063 chr18 78077248 4200617 0.05380078201526775 0.5853052878490628 chr19 59128983 3603869 0.06094928099811898 0.6163968137131209 chr20 63025520 2114090 0.03354339638927215 0.22572534623548166 chr21 48129895 1590670 0.03304952150840969 0.22865329423216066 chr22 51304566 1424111 0.027757977720735422 0.19427089913154608 chrMT 16571 20772 1.2535151771166495 1.4635567131610117 chrX 155270560 7007733 0.045132399857384424 0.2895238674875005 chrY 59373566 267198 0.004500285531106553 0.12764502068995645