BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716831.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 = 763,583 number of mapped reads = 530,914 (69.53%) number of supplementary alignments = 484 (0.06%) number of secondary alignments = 0 number of mapped bases = 27,445,943 bp number of sequenced bases = 27,438,940 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,793 duplication rate = 5.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0796 >>>>>>> ACTG content number of A's = 5,781,973 bp (21.07%) number of C's = 4,656,951 bp (16.97%) number of T's = 9,324,853 bp (33.98%) number of G's = 7,674,683 bp (27.97%) number of N's = 480 bp (0%) GC percentage = 44.94% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 198,787 number of insertions = 1,537 mapped reads with insertion percentage = 0.29% number of deletions = 4,115 mapped reads with deletion percentage = 0.77% homopolymer indels = 40.04% >>>>>>> Coverage mean coverageData = 0.0089X std coverageData = 0.1155X There is a 0.79% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 2666437 0.010697814871241584 0.12878979486859726 chr2 243199373 2334666 0.009599802710017678 0.17114330652072987 chr3 198022430 1807389 0.009127193318453875 0.10479774421543216 chr4 191154276 1686405 0.008822219598163736 0.1073866268074393 chr5 180915260 2375448 0.013130169340054565 0.12641387040175323 chr6 171115067 1121042 0.006551392695302512 0.11098375331947001 chr7 159138663 1468303 0.009226563628978082 0.11689983905817372 chr8 146364022 1630777 0.01114192530183408 0.1198618857361324 chr9 141213431 1117765 0.007915429800724834 0.10355704815191817 chr10 135534747 1324109 0.009769516890011976 0.11803736551886315 chr11 135006516 1145897 0.008487716252154822 0.1081245358963422 chr12 133851895 1282685 0.00958286769118958 0.10849326626628433 chr13 115169878 468630 0.004069032703151774 0.07020879723012834 chr14 107349540 832835 0.0077581608640335115 0.09773640583255341 chr15 102531392 709833 0.006923079713967016 0.09202487734223846 chr16 90354753 728143 0.00805871274973216 0.10390087125276451 chr17 81195210 1046687 0.01289099443181439 0.1281534946491438 chr18 78077248 689859 0.00883559574230895 0.11230466100723686 chr19 59128983 724084 0.012245838897651936 0.13617407646137455 chr20 63025520 696723 0.011054617240762154 0.12028426400449431 chr21 48129895 367195 0.007629249970314707 0.10150919231268346 chr22 51304566 288723 0.005627627763189732 0.08377226118451808 chrMT 16571 4653 0.28079174461408485 0.5926590127107944 chrX 155270560 843852 0.005434719885083174 0.08256704212057024 chrY 59373566 83803 0.001411453036187855 0.05139004605474549