BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237595.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 = 1,261,141 number of mapped reads = 967,443 (76.71%) number of supplementary alignments = 4,425 (0.35%) number of secondary alignments = 0 number of mapped bases = 60,107,233 bp number of sequenced bases = 60,070,830 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,988 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.092 >>>>>>> ACTG content number of A's = 16,148,853 bp (26.88%) number of C's = 10,443,032 bp (17.38%) number of T's = 18,968,859 bp (31.58%) number of G's = 14,397,657 bp (23.97%) number of N's = 112,429 bp (0.19%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 592,836 number of insertions = 5,823 mapped reads with insertion percentage = 0.6% number of deletions = 22,055 mapped reads with deletion percentage = 2.25% homopolymer indels = 48.58% >>>>>>> Coverage mean coverageData = 0.0194X std coverageData = 0.2092X There is a 1.68% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.04% 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 5097029 0.020449413443988974 0.2452060631292518 chr2 243199373 5223047 0.021476399941212018 0.3142542556012714 chr3 198022430 4261795 0.02152177912370836 0.17417584464892022 chr4 191154276 3946227 0.020644199452802197 0.1719422911511746 chr5 180915260 3390025 0.018738192676505012 0.1564122142777306 chr6 171115067 3239513 0.018931781150516688 0.18861283349950703 chr7 159138663 3511485 0.022065568063745766 0.2606309964531295 chr8 146364022 3126904 0.02136388408348057 0.2164420566714754 chr9 141213431 2466644 0.017467488627197224 0.20516064941275994 chr10 135534747 2605331 0.019222605698301115 0.19227913194682153 chr11 135006516 2496835 0.018494181421584127 0.19492134663938696 chr12 133851895 3569200 0.026665293009112797 0.19732870461433671 chr13 115169878 2154363 0.018705958861917 0.16691305226950762 chr14 107349540 1714334 0.015969644583479353 0.15927424103513382 chr15 102531392 1838167 0.017927845942050605 0.16008932194292985 chr16 90354753 1491553 0.016507742542332 0.1650956650042268 chr17 81195210 1329907 0.016379131232002478 0.155996842071674 chr18 78077248 1607801 0.020592439426143708 0.3788897540600439 chr19 59128983 1033488 0.01747853501894325 0.18857256289337776 chr20 63025520 1206297 0.01913981828313356 0.16391796140642137 chr21 48129895 742791 0.015433048420321714 0.15143190963579173 chr22 51304566 574880 0.01120524048483326 0.12207125207877859 chrMT 16571 43112 2.601653491038561 2.1647039916152218 chrX 155270560 3234516 0.020831482800087796 0.175601204767365 chrY 59373566 201989 0.0034020021637238365 0.08725560258230654