BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080791.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 = 2,382,445 number of mapped reads = 2,130,042 (89.41%) number of supplementary alignments = 19,921 (0.84%) number of secondary alignments = 0 number of mapped bases = 140,348,232 bp number of sequenced bases = 140,299,566 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,495 duplication rate = 3.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2165 >>>>>>> ACTG content number of A's = 40,105,364 bp (28.59%) number of C's = 26,864,998 bp (19.15%) number of T's = 43,055,578 bp (30.69%) number of G's = 30,270,779 bp (21.58%) number of N's = 2,847 bp (0%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,070,639 number of insertions = 10,496 mapped reads with insertion percentage = 0.49% number of deletions = 30,557 mapped reads with deletion percentage = 1.42% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 0.0453X std coverageData = 0.3503X There is a 3.74% of reference with a coverageData >= 1X There is a 0.59% 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% 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 18392333 0.07379052026514309 0.6695472326230711 chr2 243199373 10724634 0.04409811533519044 0.3638690021613927 chr3 198022430 7137453 0.036043659296575645 0.2210846563120215 chr4 191154276 7990994 0.04180389875244015 0.24667217939586625 chr5 180915260 11126824 0.06150296000459 0.29191908615560425 chr6 171115067 11034842 0.06448784548002427 0.36248241779645085 chr7 159138663 9450789 0.059387133345464894 0.39201328161094673 chr8 146364022 4901779 0.033490327288218415 0.4066448830939046 chr9 141213431 5526353 0.03913475482371078 0.30265765519491505 chr10 135534747 5736882 0.042327758209487046 0.3103632045878936 chr11 135006516 5006920 0.03708650625426109 0.25937218500326487 chr12 133851895 5259191 0.03929112098114113 0.23454213840862234 chr13 115169878 5054140 0.04388421771185692 0.2452394565655506 chr14 107349540 4204617 0.039167536255860995 0.2433509865472698 chr15 102531392 3875195 0.03779520519920377 0.23696275944085568 chr16 90354753 3816294 0.042236781943280836 0.2619320500062369 chr17 81195210 3597109 0.04430198530184231 0.2560567313379037 chr18 78077248 1835236 0.023505387894819242 0.529567004723416 chr19 59128983 2531198 0.04280807603269618 0.46330657864150576 chr20 63025520 2133533 0.03385189047230392 0.2213227141053558 chr21 48129895 2633144 0.054709115820842744 0.2828404247395944 chr22 51304566 1268346 0.024721893174186486 0.18534548653091149 chrMT 16571 56610 3.4162090398889626 2.657253017635355 chrX 155270560 6735040 0.043376155788966045 0.25612637606813343 chrY 59373566 318776 0.00536898861692087 0.11187264228956682