BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231850.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 = 4,958,862 number of mapped reads = 3,793,126 (76.49%) number of supplementary alignments = 40,798 (0.82%) number of secondary alignments = 0 number of mapped bases = 236,677,693 bp number of sequenced bases = 236,596,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 305,187 duplication rate = 5.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6386 >>>>>>> ACTG content number of A's = 67,498,596 bp (28.53%) number of C's = 48,917,014 bp (20.68%) number of T's = 65,895,644 bp (27.85%) number of G's = 54,265,947 bp (22.94%) number of N's = 19,014 bp (0.01%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,355,479 number of insertions = 16,137 mapped reads with insertion percentage = 0.42% number of deletions = 49,476 mapped reads with deletion percentage = 1.29% homopolymer indels = 42.86% >>>>>>> Coverage mean coverageData = 0.0765X std coverageData = 5.8436X There is a 5.51% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.11% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 12683222 0.05088541785418461 1.4479315319940982 chr2 243199373 21634301 0.08895705911215486 20.72253905598225 chr3 198022430 27964506 0.1412188811136193 0.49279021433227593 chr4 191154276 8983444 0.0469957784255896 0.3040934304614798 chr5 180915260 7258036 0.04011842892633822 0.27795074063277037 chr6 171115067 22853247 0.1335548493809724 0.5900634311576689 chr7 159138663 14928357 0.09380722898243779 0.9541053244981853 chr8 146364022 15368928 0.10500482147176853 0.5855822396051478 chr9 141213431 4727727 0.03347930127127922 0.3610766812620213 chr10 135534747 6209543 0.045815136984761556 0.48643702689842444 chr11 135006516 9765098 0.07233056810383878 0.6072234237618838 chr12 133851895 6571360 0.049094261982618924 0.2935890344797785 chr13 115169878 7464879 0.06481624474760667 0.3312877897672082 chr14 107349540 10103756 0.09412016111107696 0.4638070345793385 chr15 102531392 6316125 0.061601865309699494 0.3224787737396109 chr16 90354753 3830609 0.04239521301109638 0.3573368651194225 chr17 81195210 8294994 0.10216112502203024 0.46240843304612306 chr18 78077248 1525849 0.019542812267153677 1.1651292709165677 chr19 59128983 8364887 0.14146847409839605 0.8456684244411945 chr20 63025520 3564611 0.05655821641773047 0.3600069684646335 chr21 48129895 4805139 0.09983688931795924 0.4213292437028223 chr22 51304566 2094198 0.04081893997505017 0.2541854059286799 chrMT 16571 230084 13.884738398406855 8.630197144279917 chrX 155270560 20532208 0.13223503541173548 0.5868242768417324 chrY 59373566 602585 0.010149045115464347 0.15068293746755795