BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068941.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 = 2,132,196 number of mapped reads = 1,721,326 (80.73%) number of supplementary alignments = 13,566 (0.64%) number of secondary alignments = 0 number of mapped bases = 115,735,562 bp number of sequenced bases = 115,683,437 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,152 duplication rate = 3.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0073 >>>>>>> ACTG content number of A's = 31,924,500 bp (27.6%) number of C's = 20,749,382 bp (17.94%) number of T's = 37,593,535 bp (32.5%) number of G's = 25,128,429 bp (21.72%) number of N's = 287,591 bp (0.25%) GC percentage = 39.66% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 1,228,093 number of insertions = 11,118 mapped reads with insertion percentage = 0.64% number of deletions = 31,057 mapped reads with deletion percentage = 1.78% homopolymer indels = 48.26% >>>>>>> Coverage mean coverageData = 0.0374X std coverageData = 0.379X There is a 3.02% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 11165146 0.0447948573014789 0.7631927177314564 chr2 243199373 6734030 0.027689339478683607 0.29866693404111916 chr3 198022430 9265019 0.046787725006707574 0.25703336724346626 chr4 191154276 9955535 0.05208115250322729 0.3094344103616676 chr5 180915260 5926907 0.03276068033177522 0.2176411303654086 chr6 171115067 7079020 0.041369939679245196 0.2964675547913595 chr7 159138663 2725913 0.017129168667201884 0.21000423957132924 chr8 146364022 7243233 0.049487796939605824 0.6990457544247126 chr9 141213431 6283956 0.04449970484748012 0.3510890188993734 chr10 135534747 7476737 0.05516472465913114 0.3581419634037253 chr11 135006516 4352126 0.032236414426100736 0.26980213524119867 chr12 133851895 5442582 0.040661224856024636 0.2450720408858748 chr13 115169878 3810696 0.033087609939119675 0.21693106933668868 chr14 107349540 4296577 0.04002417709475047 0.2540867128195734 chr15 102531392 3930548 0.03833506912692651 0.23205518364280572 chr16 90354753 3080241 0.034090525376124926 0.23945967229642492 chr17 81195210 2175517 0.02679366184285994 0.2060490547989146 chr18 78077248 2293435 0.029373922093155744 0.64986722998948 chr19 59128983 2662021 0.045020578148621294 0.43366397112966815 chr20 63025520 1449190 0.022993701598971336 0.19787576957960654 chr21 48129895 946976 0.01967542210511783 0.2072131027171527 chr22 51304566 1248093 0.024327132988514123 0.18201198981373237 chrMT 16571 184742 11.148512461529178 7.152036514946545 chrX 155270560 5658576 0.036443328342475226 0.24850756277388195 chrY 59373566 348746 0.005873758702652288 0.18181803237482513