BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714116.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 814,086 number of mapped reads = 331,344 (40.7%) number of supplementary alignments = 6,317 (0.78%) number of secondary alignments = 0 number of mapped bases = 40,182,839 bp number of sequenced bases = 39,760,934 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 313,487 duplication rate = 33.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 31.2066 >>>>>>> ACTG content number of A's = 9,707,950 bp (24.42%) number of C's = 7,175,748 bp (18.05%) number of T's = 9,231,855 bp (23.22%) number of G's = 13,644,691 bp (34.32%) number of N's = 690 bp (0%) GC percentage = 52.36% >>>>>>> Mismatches and indels general error rate = 0.0319 number of mismatches = 1,108,336 number of insertions = 38,919 mapped reads with insertion percentage = 10.93% number of deletions = 95,038 mapped reads with deletion percentage = 27.61% homopolymer indels = 30.27% >>>>>>> Coverage mean coverageData = 0.013X std coverageData = 13.5044X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 504115 0.0020225225436850567 0.5877060246316167 chr2 243199373 13731892 0.056463517280531804 32.20507528297019 chr3 198022430 2276450 0.011495919931898625 8.804668546893549 chr4 191154276 305796 0.0015997340284451707 0.4174288201021632 chr5 180915260 4461030 0.024658118944747943 23.37572588995596 chr6 171115067 1118795 0.006538261180705963 2.356263967122589 chr7 159138663 534496 0.0033586809762251174 1.3383159260483877 chr8 146364022 771911 0.0052739121913444 2.4363620134331216 chr9 141213431 824251 0.005836916461579352 2.595680436214888 chr10 135534747 4569124 0.03371182741795357 22.813101298082735 chr11 135006516 1950055 0.0144441546806526 6.54315724429545 chr12 133851895 181833 0.0013584641442693061 0.4604737862591072 chr13 115169878 1282940 0.011139544664621422 4.636815184561031 chr14 107349540 4721181 0.04397951775107746 32.36641986528852 chr15 102531392 173817 0.0016952564147378396 0.5861584403261063 chr16 90354753 590517 0.0065355388664501135 4.493083214470339 chr17 81195210 84008 0.001034642314491212 0.2594380849602054 chr18 78077248 134771 0.0017261238510865547 0.4104781047835397 chr19 59128983 31028 5.247511190916306E-4 0.07075598868468762 chr20 63025520 63649 0.00100989250068861 0.2918260069247802 chr21 48129895 42452 8.820297654919048E-4 0.3091484393344044 chr22 51304566 44224 8.619895546918767E-4 0.26985315106385016 chrMT 16571 347937 20.99674129503349 169.315046510558 chrX 155270560 1415840 0.009118534769244086 2.8760852627247986 chrY 59373566 20727 3.4909474697881543E-4 0.1031600144244796