BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524881.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,494,836 number of mapped reads = 1,384,851 (92.64%) number of supplementary alignments = 5,275 (0.35%) number of secondary alignments = 0 number of mapped bases = 81,040,952 bp number of sequenced bases = 81,017,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,449 duplication rate = 2.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.209 >>>>>>> ACTG content number of A's = 21,012,944 bp (25.94%) number of C's = 15,628,567 bp (19.29%) number of T's = 25,473,329 bp (31.44%) number of G's = 18,891,708 bp (23.32%) number of N's = 10,875 bp (0.01%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 390,233 number of insertions = 6,145 mapped reads with insertion percentage = 0.44% number of deletions = 15,007 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.79% >>>>>>> Coverage mean coverageData = 0.0262X std coverageData = 0.2701X There is a 2.39% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6540058 0.02623888347303255 0.5337335625208871 chr2 243199373 6827960 0.028075565803370717 0.2820569203008721 chr3 198022430 5431579 0.027429109924567634 0.17834055602649965 chr4 191154276 5198638 0.027196033009483922 0.1929870075800544 chr5 180915260 4912336 0.027152690160022985 0.17781883085306424 chr6 171115067 4628630 0.02704980970495135 0.18764493955485062 chr7 159138663 4468619 0.028080033574242106 0.36753831330706427 chr8 146364022 4170439 0.02849360753423406 0.26007216929851595 chr9 141213431 3427032 0.024268456447319092 0.23402759365722578 chr10 135534747 3901908 0.02878898648772333 0.2545936515068279 chr11 135006516 3724998 0.027591246040302234 0.2461496144996615 chr12 133851895 3572790 0.02669211369775527 0.17977143498967843 chr13 115169878 2551216 0.022151764370194088 0.15903413053457705 chr14 107349540 2455543 0.022874275940073893 0.17037923021593696 chr15 102531392 2315221 0.022580606337618044 0.16093313198211343 chr16 90354753 2346838 0.025973597647928937 0.18926580282280986 chr17 81195210 2173998 0.026774953842720526 0.19124313838087034 chr18 78077248 2178914 0.027907156768640206 0.44986261238048975 chr19 59128983 1591858 0.026921788930481014 0.3432238338850171 chr20 63025520 1721749 0.027318283133562403 0.181195799649795 chr21 48129895 1062729 0.022080434623844493 0.17431113982021915 chr22 51304566 935737 0.01823886396388189 0.14409604418991334 chrMT 16571 14680 0.88588497978396 1.1238628668320494 chrX 155270560 4646457 0.02992490656309863 0.20970393672200605 chrY 59373566 241025 0.004059466463577411 0.10975165874535693