BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008773.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 = 1,677,234 number of mapped reads = 1,467,843 (87.52%) number of supplementary alignments = 9,200 (0.55%) number of secondary alignments = 0 number of mapped bases = 96,192,478 bp number of sequenced bases = 96,144,173 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,825 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8026 >>>>>>> ACTG content number of A's = 26,596,538 bp (27.66%) number of C's = 17,416,759 bp (18.12%) number of T's = 30,341,711 bp (31.56%) number of G's = 21,771,181 bp (22.64%) number of N's = 17,984 bp (0.02%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 758,917 number of insertions = 8,326 mapped reads with insertion percentage = 0.56% number of deletions = 29,325 mapped reads with deletion percentage = 1.97% homopolymer indels = 47.07% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.3113X There is a 2.72% 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 0.01% 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 7445743 0.02987251534269999 0.4452621673377539 chr2 243199373 9745468 0.040071928968336605 0.44935456155016673 chr3 198022430 8188385 0.04135079546291801 0.22806792725336733 chr4 191154276 6227177 0.03257670783153185 0.21064811964675104 chr5 180915260 4333590 0.023953700754706927 0.17164940762158143 chr6 171115067 6704669 0.039182224672243506 0.24264411126987673 chr7 159138663 3674680 0.023091057388109387 0.2963834858030975 chr8 146364022 7789424 0.053219526858861534 0.4396880304610367 chr9 141213431 3182569 0.022537296753309535 0.3371035788543967 chr10 135534747 4999984 0.03689079081691133 0.35547292384807466 chr11 135006516 4767237 0.03531116231456562 0.37313505243401285 chr12 133851895 4482288 0.033486922243424345 0.20648892910833516 chr13 115169878 1063443 0.009233690427283425 0.10584418386907292 chr14 107349540 3469241 0.03231724141528692 0.20557447543911037 chr15 102531392 2856587 0.027860608778236425 0.1834310767378257 chr16 90354753 2213394 0.02449670799277156 0.20706413035958862 chr17 81195210 3113452 0.03834526691907072 0.2622231245970141 chr18 78077248 2418783 0.030979357776544585 0.6128482082854388 chr19 59128983 1907642 0.0322623847597717 0.32945446199189754 chr20 63025520 1833515 0.02909162828009987 0.1934197357309164 chr21 48129895 1158400 0.024068201270748667 0.19112015936948917 chr22 51304566 1000440 0.019500018770259163 0.15137746559572435 chrMT 16571 43392 2.618550479753787 2.1142286655354883 chrX 155270560 3295480 0.021224113573107484 0.19669747120924078 chrY 59373566 277495 0.00467371287754554 0.1403382914519549