BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716978.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 = 1,794,909 number of mapped reads = 1,649,972 (91.93%) number of supplementary alignments = 8,920 (0.5%) number of secondary alignments = 0 number of mapped bases = 95,915,192 bp number of sequenced bases = 95,887,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,050 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3881 >>>>>>> ACTG content number of A's = 22,887,403 bp (23.87%) number of C's = 19,786,368 bp (20.63%) number of T's = 30,421,697 bp (31.73%) number of G's = 22,791,503 bp (23.77%) number of N's = 657 bp (0%) GC percentage = 44.4% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 481,284 number of insertions = 5,567 mapped reads with insertion percentage = 0.34% number of deletions = 17,261 mapped reads with deletion percentage = 1.04% homopolymer indels = 44.33% >>>>>>> Coverage mean coverageData = 0.031X std coverageData = 0.2897X There is a 2.73% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% 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 11478225 0.046050938424743185 0.4622339443159967 chr2 243199373 9851667 0.040508603613875274 0.42839064160824564 chr3 198022430 6089227 0.030750188248876657 0.19455298698138002 chr4 191154276 3823874 0.02000412483579494 0.17694008091040295 chr5 180915260 6578337 0.03636142689124179 0.2115249688223081 chr6 171115067 3523548 0.020591687580614977 0.18560108812775794 chr7 159138663 6534897 0.04106416930246549 0.46963299436947015 chr8 146364022 4280336 0.02924445462423819 0.24556933292520008 chr9 141213431 2689151 0.019043167359909272 0.22066351668758724 chr10 135534747 3859602 0.028476845129610934 0.23709743835784972 chr11 135006516 4148016 0.03072456147227738 0.2797323094542414 chr12 133851895 3844815 0.028724397215295308 0.18898543996257933 chr13 115169878 2752591 0.023900268436509067 0.17354375935715102 chr14 107349540 2057534 0.019166677379334834 0.16353033556761767 chr15 102531392 4424758 0.043155153886918846 0.23255201893566538 chr16 90354753 2891563 0.032002334177151696 0.20899578797285773 chr17 81195210 3710797 0.045702166420900935 0.2574261114559722 chr18 78077248 3100064 0.039705087966215205 0.5022614876006049 chr19 59128983 1544230 0.02611629562443176 0.3419913687533416 chr20 63025520 2527654 0.04010524625580241 0.22526416722430795 chr21 48129895 1236489 0.025690664814456796 0.1883262998836923 chr22 51304566 1156232 0.022536629585756557 0.1658242308987995 chrMT 16571 5133 0.3097580109830427 0.6426126880956031 chrX 155270560 3580043 0.023056804844395488 0.19199986903557628 chrY 59373566 226409 0.00381329630765314 0.09590228981874398