BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472389.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 20,594,778 number of mapped reads = 20,402,363 (99.07%) number of supplementary alignments = 99,617 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,234,791 number of mapped paired reads (second in pair) = 10,167,572 number of mapped paired reads (both in pair) = 20,288,650 number of mapped paired reads (singletons) = 113,713 number of mapped bases = 2,004,267,708 bp number of sequenced bases = 2,004,024,181 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,297,374 duplication rate = 47.47% >>>>>>> Insert size mean insert size = 24,449.2881 std insert size = 1,544,023.8892 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 54.7328 >>>>>>> ACTG content number of A's = 541,342,729 bp (27.01%) number of C's = 461,514,202 bp (23.03%) number of T's = 541,742,528 bp (27.03%) number of G's = 459,168,273 bp (22.91%) number of N's = 256,449 bp (0.01%) GC percentage = 45.94% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 11,464,400 number of insertions = 123,455 mapped reads with insertion percentage = 0.6% number of deletions = 97,359 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.86% >>>>>>> Coverage mean coverageData = 0.6474X std coverageData = 21.0368X There is a 5.36% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.73% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179984933 0.7221042510461789 20.55564048417663 chr2 243199373 149630855 0.6152600360528068 17.89270052311722 chr3 198022430 151657879 0.7658621248108106 20.657023783232408 chr4 191154276 52753312 0.27597244018752687 12.436107431128077 chr5 180915260 85117147 0.4704807488323539 22.99924014346062 chr6 171115067 150866424 0.8816665104072922 21.937872141740332 chr7 159138663 113874048 0.7155649409973992 23.93949409937626 chr8 146364022 90405847 0.6176780725525567 18.821102026219318 chr9 141213431 65913128 0.4667624568940613 12.34509446409233 chr10 135534747 47179514 0.3480990302804048 14.83583596990326 chr11 135006516 67954734 0.5033441052578529 16.07726825277873 chr12 133851895 114851785 0.8580512438766743 22.472454831118068 chr13 115169878 68903832 0.5982799773392137 21.41701518823807 chr14 107349540 32712422 0.30472810596114336 9.701290008630366 chr15 102531392 34860952 0.3400027183869697 11.529602116521977 chr16 90354753 125900042 1.3933970025904447 36.51983411428421 chr17 81195210 98449075 1.2124985574887976 35.19903082789822 chr18 78077248 35898429 0.45978092106934915 19.486958634150195 chr19 59128983 37978971 0.6423071913819319 18.486322434226135 chr20 63025520 79309209 1.2583665949919969 35.78489122522668 chr21 48129895 21741860 0.45173296139540714 22.712367393912245 chr22 51304566 19772699 0.3853984263310989 12.789336917274111 chrMT 16571 18670 1.1266670689759217 1.341423498796787 chrX 155270560 178060323 1.1467745269933978 29.60328607041636 chrY 59373566 471618 0.007943231841590919 0.5170556876132352