BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063596.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 = 1,945,202 number of mapped reads = 1,614,992 (83.02%) number of supplementary alignments = 12,916 (0.66%) number of secondary alignments = 0 number of mapped bases = 100,568,592 bp number of sequenced bases = 100,523,144 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 243,905 duplication rate = 11.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9642 >>>>>>> ACTG content number of A's = 26,819,458 bp (26.68%) number of C's = 17,897,172 bp (17.8%) number of T's = 32,987,962 bp (32.82%) number of G's = 22,816,455 bp (22.7%) number of N's = 2,097 bp (0%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 927,378 number of insertions = 8,078 mapped reads with insertion percentage = 0.5% number of deletions = 26,823 mapped reads with deletion percentage = 1.64% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.0325X std coverageData = 0.3883X There is a 1.79% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 7261456 0.029133151086512238 0.3894577059786754 chr2 243199373 7183033 0.02953557367929563 0.5033249160192549 chr3 198022430 12013433 0.06066703150749135 0.40384144214503126 chr4 191154276 5792706 0.030303826423427743 0.3065236906795725 chr5 180915260 6626171 0.03662582692029406 0.31076300361062026 chr6 171115067 5200214 0.030390158454018545 0.30424355035744866 chr7 159138663 9155605 0.057532247835964286 0.5643102017875713 chr8 146364022 4292606 0.029328286701495537 0.7103385960267947 chr9 141213431 3226849 0.022850864660316907 0.29346023408223076 chr10 135534747 7445042 0.05493087318781803 0.4767779737663714 chr11 135006516 3820568 0.02829913779865262 0.39753289523698887 chr12 133851895 4102249 0.030647672190221888 0.28633067605356644 chr13 115169878 2927640 0.02542018842808881 0.259982557813506 chr14 107349540 2462325 0.02293745273617381 0.2537335044797349 chr15 102531392 2351865 0.022937999320247208 0.2431334999576147 chr16 90354753 2494337 0.02760604082443787 0.27245129015368935 chr17 81195210 2423436 0.029847031616766554 0.29732211245767587 chr18 78077248 2202217 0.028205617595538204 0.419810154053717 chr19 59128983 1763999 0.029833068497051606 0.3727387796216956 chr20 63025520 1949065 0.030925012598071386 0.2919771347830515 chr21 48129895 1181104 0.024539924718306575 0.2608800724207553 chr22 51304566 911357 0.017763662594865337 0.20487677277947283 chrMT 16571 207089 12.49707320016897 12.655655559688167 chrX 155270560 2962492 0.01907954733981767 0.23582676941958855 chrY 59373566 611734 0.010303137258085526 0.18985912351228004