BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525242.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 = 3,513,216 number of mapped reads = 3,205,537 (91.24%) number of supplementary alignments = 10,611 (0.3%) number of secondary alignments = 0 number of mapped bases = 185,990,907 bp number of sequenced bases = 185,929,443 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 188,637 duplication rate = 4.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2748 >>>>>>> ACTG content number of A's = 47,785,321 bp (25.7%) number of C's = 30,567,540 bp (16.44%) number of T's = 60,978,458 bp (32.8%) number of G's = 46,594,354 bp (25.06%) number of N's = 3,770 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 941,351 number of insertions = 13,642 mapped reads with insertion percentage = 0.42% number of deletions = 38,377 mapped reads with deletion percentage = 1.19% homopolymer indels = 44.51% >>>>>>> Coverage mean coverageData = 0.0601X std coverageData = 0.535X There is a 5.05% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 20632351 0.08277753097353366 1.0651269294181114 chr2 243199373 16100616 0.06620336147001497 0.7748580963971782 chr3 198022430 15247734 0.07700003479403823 0.32680870234387344 chr4 191154276 10947372 0.057269825342541644 0.30418820919942435 chr5 180915260 8611723 0.047600865731282145 0.2540711079918909 chr6 171115067 9646350 0.05637346943855038 0.34454434033309544 chr7 159138663 11373773 0.07147083421204814 0.8052783524197742 chr8 146364022 8958727 0.0612085325176429 0.5221622030021049 chr9 141213431 5423231 0.038404498506944426 0.34392548799252387 chr10 135534747 8558932 0.06314935608357317 0.5135862353736176 chr11 135006516 8807647 0.06523868077597084 0.42161534624621455 chr12 133851895 8443019 0.06307732139317117 0.3000670625953273 chr13 115169878 6076445 0.05276071404712263 0.2764262111843176 chr14 107349540 7262112 0.06764921396030202 0.31680642574435314 chr15 102531392 5333760 0.05202075087403475 0.2846893623704437 chr16 90354753 5112719 0.056584947999359814 0.3255888539515357 chr17 81195210 3752777 0.04621919199420754 0.26600796864429993 chr18 78077248 4172182 0.05343659141264815 0.7741830304862032 chr19 59128983 3288406 0.055614113978588134 0.6788123075730508 chr20 63025520 3468442 0.055032342454294704 0.2802471946087529 chr21 48129895 2656830 0.05520124238791711 0.3029517855582055 chr22 51304566 1501068 0.029257980663943244 0.19446146681288215 chrMT 16571 223418 13.482469374207954 7.9955505002798954 chrX 155270560 9839460 0.06336977209330603 0.3391976967131152 chrY 59373566 551813 0.009293917094351381 0.25243215039815137