BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695933.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 15,401,036 number of mapped reads = 14,676,339 (95.29%) number of supplementary alignments = 340,359 (2.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,391,093 number of mapped paired reads (second in pair) = 7,285,246 number of mapped paired reads (both in pair) = 14,320,458 number of mapped paired reads (singletons) = 355,881 number of mapped bases = 1,295,051,113 bp number of sequenced bases = 1,294,524,777 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,361,663 duplication rate = 14.52% >>>>>>> Insert size mean insert size = 873,824.4965 std insert size = 9,125,767.1548 median insert size = 288 >>>>>>> Mapping quality mean mapping quality = 49.6836 >>>>>>> ACTG content number of A's = 348,372,383 bp (26.91%) number of C's = 289,441,831 bp (22.36%) number of T's = 356,958,854 bp (27.57%) number of G's = 299,288,206 bp (23.12%) number of N's = 463,503 bp (0.04%) GC percentage = 45.48% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 16,053,348 number of insertions = 192,324 mapped reads with insertion percentage = 1.26% number of deletions = 222,565 mapped reads with deletion percentage = 1.47% homopolymer indels = 39.07% >>>>>>> Coverage mean coverageData = 0.4183X std coverageData = 10.0976X There is a 17.84% of reference with a coverageData >= 1X There is a 8.33% of reference with a coverageData >= 2X There is a 4.49% of reference with a coverageData >= 3X There is a 2.55% of reference with a coverageData >= 4X There is a 1.49% of reference with a coverageData >= 5X There is a 0.89% of reference with a coverageData >= 6X There is a 0.55% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 109652509 0.4399287294052519 16.470069699700147 chr2 243199373 100816949 0.4145444445697646 5.379988575802427 chr3 198022430 73450421 0.3709197033891565 1.2635627558488935 chr4 191154276 81574768 0.4267483297103958 12.411334182089831 chr5 180915260 69537880 0.38436713409360823 1.6654486093904601 chr6 171115067 67819044 0.3963358995149153 7.6366585133643845 chr7 159138663 66284626 0.41652119447553737 6.717080956672932 chr8 146364022 58771707 0.4015447662404358 2.5907482470948633 chr9 141213431 53023855 0.3754873359036224 6.141317492172823 chr10 135534747 78050910 0.5758738015720796 21.616677292565086 chr11 135006516 55258654 0.40930360724218673 1.8509102057909959 chr12 133851895 60767834 0.4539930794405264 1.8856373246603946 chr13 115169878 30156106 0.26184021832514226 0.9018734459739122 chr14 107349540 36520962 0.3402060409387874 1.2575024528351129 chr15 102531392 29708437 0.2897496700327642 0.9466128745306543 chr16 90354753 60852277 0.6734817481046071 17.305143681775142 chr17 81195210 45397395 0.5591142014411934 6.171431723236095 chr18 78077248 33965511 0.4350244388736652 11.996536252164802 chr19 59128983 35345605 0.5977712317494113 19.628291492707916 chr20 63025520 29115653 0.4619660892920836 5.036982465048823 chr21 48129895 18701566 0.3885644462760619 5.222916263223635 chr22 51304566 19256189 0.3753309013470653 1.2139467400213972 chrMT 16571 10748477 648.6317663387846 1417.8596254885842 chrX 155270560 37833874 0.24366418205743573 3.529303518848583 chrY 59373566 32439904 0.5463694735802125 14.933621781758866