BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236090.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 = 1,941,967 number of mapped reads = 1,693,891 (87.23%) number of supplementary alignments = 9,953 (0.51%) number of secondary alignments = 0 number of mapped bases = 111,412,938 bp number of sequenced bases = 111,355,643 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,358 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8302 >>>>>>> ACTG content number of A's = 30,438,254 bp (27.33%) number of C's = 19,917,240 bp (17.89%) number of T's = 35,891,938 bp (32.23%) number of G's = 25,042,566 bp (22.49%) number of N's = 65,645 bp (0.06%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 902,868 number of insertions = 7,859 mapped reads with insertion percentage = 0.46% number of deletions = 33,124 mapped reads with deletion percentage = 1.93% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.3355X There is a 3.08% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 10526418 0.04223226388671666 0.5616686487294217 chr2 243199373 8486726 0.03489616726931282 0.3778261577356342 chr3 198022430 8681773 0.04384237179596271 0.23699604147092196 chr4 191154276 5954685 0.031151199568248213 0.21379247446510163 chr5 180915260 6225292 0.03440998841114896 0.211157817531288 chr6 171115067 8827736 0.05158947224676597 0.3232828097659697 chr7 159138663 6159956 0.038708104516373874 0.41747701707445933 chr8 146364022 7884518 0.05386923570602617 0.5730707675450106 chr9 141213431 5299817 0.03753054481057117 0.3218440759493851 chr10 135534747 3872313 0.028570629198134703 0.2877500179243835 chr11 135006516 4356254 0.03226699072806234 0.263840163529844 chr12 133851895 3940196 0.029436983316523085 0.20236522203972934 chr13 115169878 4033356 0.0350209279547904 0.21123870388361432 chr14 107349540 3125699 0.029117022765071932 0.21040674973626364 chr15 102531392 2847278 0.02776981707221921 0.19740354904156399 chr16 90354753 3675102 0.040674141403496504 0.24588291247748728 chr17 81195210 2588985 0.03188593268001893 0.2468346048521327 chr18 78077248 3082404 0.03947890171538833 0.5131604642983163 chr19 59128983 1611015 0.02724577556153807 0.4062944433597764 chr20 63025520 1936746 0.030729552092549177 0.20132517639180836 chr21 48129895 1791482 0.037221814009775006 0.23421491969230201 chr22 51304566 906606 0.01767105875137897 0.14823142370636969 chrMT 16571 175325 10.580230523203186 6.849185223102278 chrX 155270560 5180472 0.033364161242156916 0.23185005491176203 chrY 59373566 242784 0.004089092442249469 0.1072426827815491