BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524732.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 = 1,383,056 number of mapped reads = 1,244,865 (90.01%) number of supplementary alignments = 4,799 (0.35%) number of secondary alignments = 0 number of mapped bases = 70,792,696 bp number of sequenced bases = 70,770,348 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,122 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.377 >>>>>>> ACTG content number of A's = 16,882,990 bp (23.86%) number of C's = 14,189,983 bp (20.05%) number of T's = 23,068,227 bp (32.6%) number of G's = 16,621,122 bp (23.49%) number of N's = 8,026 bp (0.01%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 368,199 number of insertions = 4,866 mapped reads with insertion percentage = 0.39% number of deletions = 13,986 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.79% >>>>>>> Coverage mean coverageData = 0.0229X std coverageData = 0.2161X There is a 2.06% of reference with a coverageData >= 1X There is a 0.17% 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 5700694 0.022871333187169874 0.2698575245076203 chr2 243199373 5917564 0.02433215154711768 0.35874654433276426 chr3 198022430 4652941 0.023497040209030866 0.1681610484208045 chr4 191154276 4514117 0.023615045890995397 0.18749998873124962 chr5 180915260 4167938 0.02303806765664765 0.1649685718837617 chr6 171115067 4026656 0.023531861165679818 0.18378629299630028 chr7 159138663 3873884 0.024342821077992845 0.25121389603790273 chr8 146364022 3495335 0.023881107885925682 0.19979947925023683 chr9 141213431 3029165 0.021450969490288782 0.18882849029385448 chr10 135534747 3479895 0.02567529786291629 0.2613221833938079 chr11 135006516 3183261 0.023578573051985137 0.19094233836660912 chr12 133851895 3203404 0.023932451610042576 0.17047890674286578 chr13 115169878 2177107 0.018903441054265942 0.1502365541676658 chr14 107349540 2122948 0.01977603257545398 0.15588782632739365 chr15 102531392 2040858 0.01990471367052151 0.15496052474480412 chr16 90354753 2177657 0.02410118923129589 0.18376706044101926 chr17 81195210 2020626 0.024886024680519946 0.17703398096466438 chr18 78077248 1898915 0.02432097760412867 0.27331790672423883 chr19 59128983 1597808 0.02702241640110739 0.2402278908822651 chr20 63025520 1496824 0.023749490682504485 0.17644286435814438 chr21 48129895 942721 0.019587015512915622 0.16593680130866062 chr22 51304566 887250 0.01729378238966099 0.1444101936981245 chrMT 16571 34879 2.104821676422666 1.8048835000697865 chrX 155270560 3914146 0.025208552091265723 0.18339436311154286 chrY 59373566 236103 0.003976567619334167 0.11873686681277949