BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714095.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 544,062 number of mapped reads = 392,331 (72.11%) number of supplementary alignments = 14,330 (2.63%) number of secondary alignments = 0 number of mapped bases = 50,992,502 bp number of sequenced bases = 49,804,886 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 339,289 duplication rate = 43.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.0951 >>>>>>> ACTG content number of A's = 13,801,444 bp (27.71%) number of C's = 10,049,554 bp (20.18%) number of T's = 13,049,831 bp (26.2%) number of G's = 12,903,630 bp (25.91%) number of N's = 427 bp (0%) GC percentage = 46.09% >>>>>>> Mismatches and indels general error rate = 0.0466 number of mismatches = 2,166,619 number of insertions = 56,600 mapped reads with insertion percentage = 13.81% number of deletions = 191,853 mapped reads with deletion percentage = 45.11% homopolymer indels = 29.65% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 4.1658X There is a 0.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 3749200 0.015041888300852017 2.422761582482133 chr2 243199373 6303575 0.02591937192206495 11.39329397468292 chr3 198022430 3496280 0.017655979678665695 4.588418133545595 chr4 191154276 1932666 0.010110503622738735 1.7206813405992927 chr5 180915260 2346218 0.012968601985260945 2.512443361921764 chr6 171115067 2404037 0.014049242081061161 2.725649415873295 chr7 159138663 2191473 0.01377083958534954 2.330310828402533 chr8 146364022 2676398 0.018285900888949335 3.994146996632229 chr9 141213431 1477119 0.010460187742340175 2.010132965078311 chr10 135534747 2414535 0.01781487812863221 3.13916428316572 chr11 135006516 2728072 0.02020696541787657 2.9252541749885315 chr12 133851895 2065865 0.015433961543839182 2.5539465506355583 chr13 115169878 1232899 0.010705047373584957 1.6710808791559648 chr14 107349540 1484870 0.013832103984795835 2.0754741150117804 chr15 102531392 1068661 0.010422768862827884 1.149137668655688 chr16 90354753 1337046 0.01479773842113209 2.055473956509833 chr17 81195210 1652563 0.020352961707962823 3.9171769349935333 chr18 78077248 1210119 0.015498996583486139 2.2645851244226924 chr19 59128983 996892 0.016859616881961255 2.358193626987589 chr20 63025520 1047002 0.016612350044870713 2.2196544100145092 chr21 48129895 447616 0.009300165728597579 2.1892702988138666 chr22 51304566 638938 0.012453823310775108 2.1989873129525983 chrMT 16571 299007 18.043992517047855 142.17091501171686 chrX 155270560 5303605 0.03415718343515989 3.2068786044601207 chrY 59373566 487846 0.008216552126917895 2.6170811266748975