BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240188.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,715,629 number of mapped reads = 1,477,067 (86.09%) number of supplementary alignments = 14,310 (0.83%) number of secondary alignments = 0 number of mapped bases = 98,139,371 bp number of sequenced bases = 98,077,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,579 duplication rate = 4.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1023 >>>>>>> ACTG content number of A's = 28,531,470 bp (29.09%) number of C's = 18,357,862 bp (18.72%) number of T's = 30,717,755 bp (31.32%) number of G's = 20,395,919 bp (20.8%) number of N's = 74,246 bp (0.08%) GC percentage = 39.51% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 951,425 number of insertions = 6,921 mapped reads with insertion percentage = 0.46% number of deletions = 35,745 mapped reads with deletion percentage = 2.39% homopolymer indels = 44.86% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 0.3527X There is a 2.41% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% 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% 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 11597651 0.04653007865525037 0.5799391752325321 chr2 243199373 14893499 0.061239874166945325 0.3718052255448377 chr3 198022430 5351451 0.027024468894761063 0.20842584497929992 chr4 191154276 7235969 0.037854078660526536 0.2522553450066213 chr5 180915260 8086326 0.04469676024012568 0.2676922970899295 chr6 171115067 2005861 0.011722293279995034 0.14338447333490853 chr7 159138663 1952441 0.01226880359048888 0.20746431192762066 chr8 146364022 1963290 0.013413747266387638 0.8299545555017743 chr9 141213431 3014762 0.021348974942758808 0.27306569167431877 chr10 135534747 5278674 0.03894701629538586 0.38471433037380726 chr11 135006516 3105288 0.023001023150615932 0.2605612191003657 chr12 133851895 6020055 0.044975493249460534 0.2716037702665286 chr13 115169878 3870778 0.03360929148505306 0.22825763809513502 chr14 107349540 3502245 0.032624685676342906 0.24549842268327196 chr15 102531392 903597 0.008812881424647 0.12011716017010005 chr16 90354753 2955863 0.03271397355266967 0.25340626073890327 chr17 81195210 1328283 0.01635913005212992 0.17322606742185326 chr18 78077248 2403197 0.030779734961969972 0.5222382898412289 chr19 59128983 1049783 0.017754118991020022 0.37289099227115835 chr20 63025520 1375307 0.021821430430086098 0.19511579932384854 chr21 48129895 1682501 0.03495750406270365 0.248129018480795 chr22 51304566 1677202 0.032691086403498666 0.22389845646705575 chrMT 16571 19118 1.1537022509202823 1.3725478585269926 chrX 155270560 6587994 0.04242912500605395 0.27752381391186054 chrY 59373566 278236 0.004686193178964525 0.10837720069948496