BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695932.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 = 15,634,480 number of mapped reads = 14,819,848 (94.79%) number of supplementary alignments = 233,545 (1.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,452,929 number of mapped paired reads (second in pair) = 7,366,919 number of mapped paired reads (both in pair) = 14,518,960 number of mapped paired reads (singletons) = 300,888 number of mapped bases = 1,310,949,238 bp number of sequenced bases = 1,310,518,176 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,516,857 duplication rate = 16.06% >>>>>>> Insert size mean insert size = 399,846.1694 std insert size = 6,107,694.8642 median insert size = 287 >>>>>>> Mapping quality mean mapping quality = 51.2019 >>>>>>> ACTG content number of A's = 355,477,051 bp (27.12%) number of C's = 290,457,823 bp (22.16%) number of T's = 361,538,828 bp (27.59%) number of G's = 302,573,370 bp (23.09%) number of N's = 471,104 bp (0.04%) GC percentage = 45.25% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 13,632,936 number of insertions = 142,083 mapped reads with insertion percentage = 0.93% number of deletions = 193,705 mapped reads with deletion percentage = 1.27% homopolymer indels = 41.34% >>>>>>> Coverage mean coverageData = 0.4235X std coverageData = 7.1233X There is a 17.28% of reference with a coverageData >= 1X There is a 8.55% of reference with a coverageData >= 2X There is a 4.97% of reference with a coverageData >= 3X There is a 3.09% of reference with a coverageData >= 4X There is a 1.96% of reference with a coverageData >= 5X There is a 1.26% of reference with a coverageData >= 6X There is a 0.82% of reference with a coverageData >= 7X There is a 0.54% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% 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 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 97793901 0.39235168445177115 10.081796872173902 chr2 243199373 108941107 0.44794978562712 3.664702118421427 chr3 198022430 77069336 0.3891949815988017 1.2119874431135063 chr4 191154276 82579903 0.4320065693952878 7.08907754372426 chr5 180915260 66736645 0.3688834485272276 1.3926805673355542 chr6 171115067 75122941 0.43902002504548593 6.61223451758822 chr7 159138663 71848744 0.451485155433284 5.003308242738218 chr8 146364022 59411516 0.40591612056137677 2.1748148988517513 chr9 141213431 50522457 0.35777373754200475 3.9247598128526606 chr10 135534747 73357075 0.541241833726963 13.809482448350611 chr11 135006516 70831823 0.5246548470297537 1.7162185002762471 chr12 133851895 58135989 0.4343307130616268 1.661636434477447 chr13 115169878 33019736 0.2867046190671488 1.0125558375970136 chr14 107349540 42822655 0.39890860268241485 1.3275387923581983 chr15 102531392 37328746 0.364071386059013 1.1513145847777395 chr16 90354753 53255092 0.5894000064390635 11.096666578498155 chr17 81195210 39567810 0.4873170473972541 4.6031011314323225 chr18 78077248 34360410 0.44008223752968345 9.245770803288716 chr19 59128983 30660269 0.5185319862511418 12.28489868892744 chr20 63025520 37979752 0.6026091018368432 3.0512608805501373 chr21 48129895 18031896 0.37465064072963383 3.4231797842040628 chr22 51304566 20760250 0.40464721989851743 1.3192269458909485 chrMT 16571 10950717 660.8362199022389 1435.032922252655 chrX 155270560 40353680 0.25989266735432653 2.8714978980821666 chrY 59373566 19506788 0.328543311681835 8.711061074289868