BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716138.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 = 1,944,410 number of mapped reads = 1,747,469 (89.87%) number of supplementary alignments = 11,551 (0.59%) number of secondary alignments = 0 number of mapped bases = 100,499,132 bp number of sequenced bases = 100,470,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,657 duplication rate = 2.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2981 >>>>>>> ACTG content number of A's = 25,264,627 bp (25.15%) number of C's = 17,238,573 bp (17.16%) number of T's = 31,820,581 bp (31.67%) number of G's = 26,145,382 bp (26.02%) number of N's = 1,400 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 557,877 number of insertions = 7,097 mapped reads with insertion percentage = 0.4% number of deletions = 16,962 mapped reads with deletion percentage = 0.96% homopolymer indels = 44.05% >>>>>>> Coverage mean coverageData = 0.0325X std coverageData = 0.3243X There is a 2.89% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7301217 0.02929267325676994 0.5350422639324253 chr2 243199373 8370462 0.034418106826286925 0.38065878204791603 chr3 198022430 5957200 0.03008346074735069 0.18794061703863257 chr4 191154276 6246552 0.03267806575250244 0.23362473904083936 chr5 180915260 5431689 0.030023387745179705 0.19275324378376282 chr6 171115067 5195259 0.030361201331265585 0.21589134926926754 chr7 159138663 6504471 0.0408729775491453 0.44340931072427725 chr8 146364022 4349026 0.02971376394671636 0.2879715094588721 chr9 141213431 4663368 0.03302354433977318 0.3715467003597719 chr10 135534747 3905680 0.028816816989373214 0.3310538257295819 chr11 135006516 3828336 0.028356675762227654 0.27453990620145624 chr12 133851895 7286787 0.054439176972429115 0.28709396793689695 chr13 115169878 3694154 0.03207569604267532 0.1924244071449423 chr14 107349540 3533901 0.03291957282723335 0.23491977502994996 chr15 102531392 2561983 0.02498730340069898 0.17333410767038515 chr16 90354753 2901189 0.0321088698012378 0.22817075939471868 chr17 81195210 3081445 0.03795106878841745 0.2224656268236758 chr18 78077248 3123704 0.04000786503130848 0.672500252677617 chr19 59128983 1848287 0.03125856231959883 0.4437649877484161 chr20 63025520 2953907 0.046868427265653656 0.24927824057405862 chr21 48129895 1180066 0.024518358080772875 0.21260768572494262 chr22 51304566 991738 0.01933040423731486 0.14912022397537275 chrMT 16571 6042 0.3646128779192565 0.7219390264004734 chrX 155270560 5273375 0.03396249102212293 0.2596689989669651 chrY 59373566 309294 0.005209287917791564 0.1355195292231905