BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240228.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 = 1,070,526 number of mapped reads = 767,761 (71.72%) number of supplementary alignments = 5,556 (0.52%) number of secondary alignments = 0 number of mapped bases = 47,783,940 bp number of sequenced bases = 47,764,613 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,980 duplication rate = 5.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4121 >>>>>>> ACTG content number of A's = 13,041,558 bp (27.3%) number of C's = 8,384,798 bp (17.55%) number of T's = 15,485,799 bp (32.42%) number of G's = 10,840,714 bp (22.7%) number of N's = 11,744 bp (0.02%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 392,000 number of insertions = 3,263 mapped reads with insertion percentage = 0.42% number of deletions = 11,407 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 0.1989X There is a 1.27% of reference with a coverageData >= 1X There is a 0.2% 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 3282053 0.013167682338492548 0.23273798441847768 chr2 243199373 3686667 0.015159031680562762 0.21304928921379637 chr3 198022430 3246415 0.016394178174664355 0.15055304044584542 chr4 191154276 2895274 0.015146268556398916 0.1479649883944632 chr5 180915260 2438759 0.013480117708146897 0.13769853880021912 chr6 171115067 4254743 0.024864806323571728 0.23134895123517474 chr7 159138663 2321064 0.014585167150738222 0.18839725198575327 chr8 146364022 2983770 0.02038595249862702 0.3667274347969198 chr9 141213431 2654558 0.0187981977436693 0.23021440329912835 chr10 135534747 1893619 0.013971465191874376 0.17751786196893987 chr11 135006516 2330800 0.017264351892467174 0.18423926789484477 chr12 133851895 1886373 0.014092986879266819 0.1458611379534841 chr13 115169878 2463598 0.02139099253018224 0.1719943107381663 chr14 107349540 1971233 0.018362752183195195 0.17528473833971356 chr15 102531392 1065713 0.010394016692955851 0.12358268779791505 chr16 90354753 1201704 0.013299842676787573 0.1503986715081767 chr17 81195210 987433 0.012161222318410162 0.133404690717394 chr18 78077248 1104655 0.01414823176144733 0.3845917295637506 chr19 59128983 668457 0.011305065064284971 0.18008827119395857 chr20 63025520 870946 0.01381894191432296 0.14353328922547928 chr21 48129895 766484 0.01592532042714824 0.15596761896472291 chr22 51304566 365559 0.007125272241850755 0.0972835014219557 chrMT 16571 17515 1.056966990525617 1.545246627601212 chrX 155270560 2302314 0.014827756143856247 0.15312871538422126 chrY 59373566 124234 0.0020924126403322313 0.06013692470565178