BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234133.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 = 1,921,880 number of mapped reads = 1,280,069 (66.61%) number of supplementary alignments = 5,282 (0.27%) number of secondary alignments = 0 number of mapped bases = 78,136,280 bp number of sequenced bases = 78,083,178 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,727 duplication rate = 4.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6153 >>>>>>> ACTG content number of A's = 20,275,875 bp (25.97%) number of C's = 13,777,698 bp (17.64%) number of T's = 24,776,186 bp (31.73%) number of G's = 19,235,811 bp (24.64%) number of N's = 17,608 bp (0.02%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 724,657 number of insertions = 6,634 mapped reads with insertion percentage = 0.51% number of deletions = 30,047 mapped reads with deletion percentage = 2.31% homopolymer indels = 47.12% >>>>>>> Coverage mean coverageData = 0.0252X std coverageData = 0.2565X There is a 2.08% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.06% 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% 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 6787170 0.027230303269735887 0.3938478058362043 chr2 243199373 5513657 0.02267134545614145 0.2913384388132584 chr3 198022430 6544290 0.03304822590046996 0.2156611043513443 chr4 191154276 4040407 0.021136890497809216 0.1843490261898606 chr5 180915260 4649966 0.025702453181671907 0.1930170005922951 chr6 171115067 5013771 0.02930058169570772 0.24464125813264787 chr7 159138663 4534210 0.02849219614217822 0.36034109752559773 chr8 146364022 3642833 0.024888855541288692 0.2923608883565638 chr9 141213431 3146695 0.022283255761982017 0.24439536767352626 chr10 135534747 3728750 0.027511395288176543 0.23142658273840475 chr11 135006516 3594905 0.026627640698468215 0.26421468089089023 chr12 133851895 3044039 0.02274184463357803 0.1812590101842628 chr13 115169878 2829158 0.024565086367461464 0.20065141248934157 chr14 107349540 3228859 0.030077995676553435 0.21802101803410964 chr15 102531392 1895306 0.018485128925197856 0.17049360070103328 chr16 90354753 2104501 0.023291536196219806 0.19939078446394004 chr17 81195210 2179073 0.026837457529822265 0.21429639220980856 chr18 78077248 1904020 0.02438636156848151 0.37312673131041585 chr19 59128983 2300475 0.03890604714104418 0.3068493013081505 chr20 63025520 1807497 0.028678811376724858 0.2126827465428154 chr21 48129895 1142724 0.02374249933435342 0.19066062625184346 chr22 51304566 877310 0.017100037450857686 0.15433125024773925 chrMT 16571 44889 2.7088890229919738 3.3363741344288425 chrX 155270560 3266692 0.021038708174943143 0.19004837810895855 chrY 59373566 315083 0.005306789219970382 0.1032320258625632