BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234139.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 = 1,931,899 number of mapped reads = 1,702,454 (88.12%) number of supplementary alignments = 14,762 (0.76%) number of secondary alignments = 0 number of mapped bases = 112,107,857 bp number of sequenced bases = 112,063,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,124 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9464 >>>>>>> ACTG content number of A's = 29,928,270 bp (26.71%) number of C's = 21,476,980 bp (19.17%) number of T's = 33,595,783 bp (29.98%) number of G's = 27,034,824 bp (24.12%) number of N's = 27,573 bp (0.02%) GC percentage = 43.29% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 936,578 number of insertions = 9,788 mapped reads with insertion percentage = 0.57% number of deletions = 25,997 mapped reads with deletion percentage = 1.51% homopolymer indels = 44.27% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.5581X There is a 3.23% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 0.01% 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 9323256 0.037405146525191606 1.2572670379905093 chr2 243199373 9724164 0.03998433005828514 0.6557820355232682 chr3 198022430 7203686 0.0363781315076277 0.2112807737142953 chr4 191154276 7068175 0.036976285060973474 0.25638720287459843 chr5 180915260 6806316 0.03762156934688649 0.21690561160397545 chr6 171115067 6328710 0.03698511247989635 0.2918778705553429 chr7 159138663 6467963 0.040643567553410954 0.8379487210345338 chr8 146364022 5624939 0.038431158990697864 0.5684513628878988 chr9 141213431 4875759 0.034527586827063216 0.4802045259543631 chr10 135534747 5103103 0.037651621543219466 0.4228865977882551 chr11 135006516 4920147 0.036443774313826456 0.4511373248147157 chr12 133851895 5005211 0.03739365064648506 0.2235373429919598 chr13 115169878 3307436 0.028717890974930094 0.1827865366275254 chr14 107349540 3419337 0.031852367508980475 0.2528337091826739 chr15 102531392 3067142 0.029914174967994193 0.22063775612872139 chr16 90354753 3098015 0.03428723887939797 0.2607812122811576 chr17 81195210 3030707 0.03732617970936956 0.27931359949456314 chr18 78077248 2935245 0.03759411448518268 0.9946481375318393 chr19 59128983 2621518 0.044335584124624634 0.8492056535466252 chr20 63025520 2163702 0.034330569585145826 0.23276337396966337 chr21 48129895 1428285 0.029675630915047706 0.22785309750180768 chr22 51304566 1244180 0.02425086297387254 0.1663760392012872 chrMT 16571 16159 0.9751372880333112 1.0209251332064855 chrX 155270560 6947379 0.044743697710628465 0.2985834282316518 chrY 59373566 377323 0.006355067169116977 0.16611906360738235