BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524471.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 = 1,427,309 number of mapped reads = 1,306,403 (91.53%) number of supplementary alignments = 2,985 (0.21%) number of secondary alignments = 0 number of mapped bases = 75,967,878 bp number of sequenced bases = 75,943,077 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,669 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0676 >>>>>>> ACTG content number of A's = 19,443,609 bp (25.6%) number of C's = 13,462,631 bp (17.73%) number of T's = 23,709,505 bp (31.22%) number of G's = 19,325,726 bp (25.45%) number of N's = 1,606 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 356,778 number of insertions = 4,896 mapped reads with insertion percentage = 0.37% number of deletions = 14,427 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.9% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.2393X There is a 2.21% of reference with a coverageData >= 1X There is a 0.18% 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 7475152 0.029990505018641457 0.4299780896162633 chr2 243199373 5936017 0.024408027565103962 0.2588354752456049 chr3 198022430 4204839 0.02123415514091005 0.1609561840718575 chr4 191154276 4289877 0.022441962009785228 0.182504975383155 chr5 180915260 4188028 0.02314911412116369 0.16606852072202274 chr6 171115067 3251556 0.01900216069225511 0.19051216671255283 chr7 159138663 3780588 0.023756565052956365 0.30922076901230294 chr8 146364022 6995868 0.04779772996399347 0.2675660190958344 chr9 141213431 3244554 0.022976242252764185 0.21214615412594742 chr10 135534747 4001337 0.029522591723287018 0.25574281206534194 chr11 135006516 2618761 0.019397293386935487 0.21668686300551943 chr12 133851895 3501725 0.026161191068680797 0.1763517771196348 chr13 115169878 1689700 0.014671370929124367 0.13205007534590144 chr14 107349540 1812980 0.01688856794356082 0.14443497490530874 chr15 102531392 2044255 0.019937844987026023 0.15886006634746852 chr16 90354753 2396452 0.026522699918176965 0.18908001551134965 chr17 81195210 2654441 0.032692088609660594 0.2047798001222075 chr18 78077248 1803374 0.023097304864023897 0.3479679426136521 chr19 59128983 1534294 0.025948256204575682 0.3144692426305985 chr20 63025520 2117327 0.03359475653671719 0.20135041116706837 chr21 48129895 1025499 0.021306902913459505 0.1685806503188165 chr22 51304566 603464 0.011762383878269236 0.11723269348932078 chrMT 16571 3524 0.2126606722587653 0.47937417162560864 chrX 155270560 4553481 0.029326106636055154 0.2036186419600808 chrY 59373566 240785 0.0040554242606886705 0.11852644884294512