BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716455.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,311,632 number of mapped reads = 1,193,329 (90.98%) number of supplementary alignments = 4,218 (0.32%) number of secondary alignments = 0 number of mapped bases = 69,277,610 bp number of sequenced bases = 69,254,747 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,989 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.711 >>>>>>> ACTG content number of A's = 17,488,699 bp (25.25%) number of C's = 12,851,791 bp (18.56%) number of T's = 22,463,746 bp (32.44%) number of G's = 16,449,222 bp (23.75%) number of N's = 1,289 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 351,629 number of insertions = 4,939 mapped reads with insertion percentage = 0.41% number of deletions = 14,097 mapped reads with deletion percentage = 1.17% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 0.0224X std coverageData = 0.2291X There is a 2.03% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 5825866 0.023373526519719284 0.3356516563988861 chr2 243199373 5446237 0.022394124346693935 0.342265206775481 chr3 198022430 3968169 0.02003898750257736 0.15281019392073067 chr4 191154276 4295058 0.022469065771774835 0.19782497038220348 chr5 180915260 3938941 0.021772298257206165 0.15879919029037654 chr6 171115067 3654920 0.021359428272905975 0.17940938331898296 chr7 159138663 3909799 0.02456850476367267 0.27291004465403634 chr8 146364022 3656510 0.024982300636696087 0.30074757721378303 chr9 141213431 2309126 0.016352028158001488 0.16553536179119352 chr10 135534747 3064692 0.02261185465598722 0.24448533213322815 chr11 135006516 2460386 0.01822420186000504 0.1796611745205791 chr12 133851895 3387829 0.025310280440930626 0.17386067759125284 chr13 115169878 2062142 0.017905219974271396 0.1452076740484265 chr14 107349540 2336901 0.021769082568961172 0.1618925289267367 chr15 102531392 2577746 0.025141041682141603 0.17206190639016397 chr16 90354753 2346461 0.02596942520555615 0.18065594795759243 chr17 81195210 3027148 0.03728234707441486 0.21635054435738593 chr18 78077248 1284450 0.016451015281686156 0.25014204523230416 chr19 59128983 1778902 0.030085110714655788 0.2728215452960058 chr20 63025520 2294705 0.03640914029745411 0.2123712760860143 chr21 48129895 885605 0.018400310243768453 0.18401455005799952 chr22 51304566 653208 0.012731966195757314 0.12139199856805827 chrMT 16571 117700 7.102769899221531 5.103084624141985 chrX 155270560 3716767 0.02393735811862854 0.17806606989799073 chrY 59373566 278342 0.004687978485240385 0.20323447077649828