BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240271.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 = 2,655,931 number of mapped reads = 2,196,323 (82.7%) number of supplementary alignments = 20,671 (0.78%) number of secondary alignments = 0 number of mapped bases = 139,406,267 bp number of sequenced bases = 139,354,429 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 334,998 duplication rate = 11.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3454 >>>>>>> ACTG content number of A's = 38,132,121 bp (27.36%) number of C's = 25,509,542 bp (18.31%) number of T's = 44,249,142 bp (31.75%) number of G's = 31,429,139 bp (22.55%) number of N's = 34,485 bp (0.02%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,091,966 number of insertions = 9,584 mapped reads with insertion percentage = 0.43% number of deletions = 30,631 mapped reads with deletion percentage = 1.38% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.4572X There is a 2.4% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 10021722 0.04020741035586026 0.7241726940779268 chr2 243199373 13297935 0.05467915001573627 0.5754900108754271 chr3 198022430 8982426 0.04536064929614286 0.36271108431990245 chr4 191154276 9167638 0.047959366600828744 0.38336231230242956 chr5 180915260 8434602 0.046621838312589 0.3630439834761938 chr6 171115067 9245122 0.054028684686194234 0.4565896835531014 chr7 159138663 6944473 0.04363787447428787 0.4753669418007255 chr8 146364022 7785634 0.053193632517149605 0.5396259803990793 chr9 141213431 5435076 0.03848837863021684 0.3989697345962645 chr10 135534747 6449079 0.047582477134073965 0.46813616728909946 chr11 135006516 7106569 0.052638711156726685 0.42125618362396317 chr12 133851895 6307139 0.04712028171136464 0.3725249003896154 chr13 115169878 3838163 0.033326101118210785 0.30900711734537034 chr14 107349540 4540378 0.0422952720617154 0.3651138290257474 chr15 102531392 3935222 0.03838065516559065 0.3671354953478656 chr16 90354753 4157878 0.046017258217727626 0.3704993909278801 chr17 81195210 3129988 0.038548924253043994 0.33931876045546133 chr18 78077248 3707086 0.04747972162133583 0.5966081081630196 chr19 59128983 2598803 0.043951423957351 0.5252607028740287 chr20 63025520 2756959 0.04374353436512701 0.35692660661234077 chr21 48129895 1826557 0.037950571053604006 0.3329014074865487 chr22 51304566 1324699 0.02582029443539197 0.26482097482769984 chrMT 16571 33540 2.0240178625309273 2.8475923853234897 chrX 155270560 7991666 0.05146929334189301 0.40428376712448616 chrY 59373566 387913 0.006533429371582633 0.13919817620233793