BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240072.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 = 2,274,370 number of mapped reads = 2,077,181 (91.33%) number of supplementary alignments = 15,141 (0.67%) number of secondary alignments = 0 number of mapped bases = 143,367,335 bp number of sequenced bases = 143,312,183 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,162 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6079 >>>>>>> ACTG content number of A's = 41,697,870 bp (29.1%) number of C's = 26,803,595 bp (18.7%) number of T's = 45,297,448 bp (31.61%) number of G's = 29,499,212 bp (20.58%) number of N's = 14,058 bp (0.01%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,141,810 number of insertions = 11,303 mapped reads with insertion percentage = 0.54% number of deletions = 31,311 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 0.0463X std coverageData = 0.59X There is a 3.94% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 11124486 0.04463172831974609 0.8099813340521472 chr2 243199373 11279703 0.04638047730493121 0.492259475717615 chr3 198022430 8895168 0.04492000224419022 0.23745843796333793 chr4 191154276 9833974 0.05144522113646048 0.2769604293720523 chr5 180915260 8504454 0.047007941729183045 0.24977244765956041 chr6 171115067 8296729 0.048486256327153233 0.3072007519791974 chr7 159138663 8498601 0.05340374764867793 0.4793654842497547 chr8 146364022 7731769 0.05282561174767389 1.8660778375103855 chr9 141213431 5340330 0.037817436784748894 0.45747633373299806 chr10 135534747 6672504 0.04923094739683249 0.3502607784283983 chr11 135006516 7799659 0.05777246336761997 0.48878597653938505 chr12 133851895 5783028 0.043204677826937 0.24547349424847612 chr13 115169878 4527057 0.039307647786168534 0.22168765450355593 chr14 107349540 4691660 0.043704518901524866 0.2727179127481336 chr15 102531392 4735216 0.04618308507895806 0.24164600289204177 chr16 90354753 3352237 0.03710083740697072 0.2791681585460543 chr17 81195210 3665189 0.045140458408815004 0.31025590541365694 chr18 78077248 4124937 0.052831485556458134 1.0574218940253146 chr19 59128983 2379803 0.040247656551102864 0.5190497209506452 chr20 63025520 2578898 0.04091831372434531 0.24549253006494565 chr21 48129895 2019639 0.04196225651437636 0.2636513461954962 chr22 51304566 1513826 0.02950665248781171 0.190118544051593 chrMT 16571 79127 4.775028664534427 3.7389590210407904 chrX 155270560 9535009 0.061408994725078596 0.3558132312407098 chrY 59373566 404332 0.006809966576708564 0.1729328722420641