BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716600.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 = 1,011,433 number of mapped reads = 857,247 (84.76%) number of supplementary alignments = 5,233 (0.52%) number of secondary alignments = 0 number of mapped bases = 49,974,634 bp number of sequenced bases = 49,960,228 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,706 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.873 >>>>>>> ACTG content number of A's = 12,978,495 bp (25.98%) number of C's = 9,408,217 bp (18.83%) number of T's = 15,158,317 bp (30.34%) number of G's = 12,414,559 bp (24.85%) number of N's = 640 bp (0%) GC percentage = 43.68% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 246,956 number of insertions = 3,395 mapped reads with insertion percentage = 0.39% number of deletions = 9,063 mapped reads with deletion percentage = 1.05% homopolymer indels = 40.02% >>>>>>> Coverage mean coverageData = 0.0161X std coverageData = 0.1631X There is a 1.51% of reference with a coverageData >= 1X There is a 0.08% 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 3837111 0.015394589528424886 0.23855266396744224 chr2 243199373 4078617 0.016770672348731756 0.19775255959184668 chr3 198022430 3214030 0.016230636095113063 0.133944773573745 chr4 191154276 3062190 0.016019469007326835 0.14290884039127763 chr5 180915260 2909607 0.016082706345501203 0.13358410985755592 chr6 171115067 2804900 0.016391893765848216 0.14035265709212605 chr7 159138663 2696162 0.01694221849783921 0.1954996994999872 chr8 146364022 2504259 0.017109799018777988 0.16951904405019763 chr9 141213431 2027572 0.014358209312257274 0.13968496538366457 chr10 135534747 2368894 0.017478130534304977 0.16871555562214885 chr11 135006516 2262221 0.01675638381780032 0.15758375138430172 chr12 133851895 2199506 0.016432385959122955 0.13502586998194752 chr13 115169878 1529377 0.013279314231799394 0.12153580608011808 chr14 107349540 1495671 0.013932719227301766 0.12687828222276082 chr15 102531392 1435402 0.013999634375392075 0.1260285904432149 chr16 90354753 1465068 0.01621462016502884 0.13742843195451498 chr17 81195210 1356412 0.016705566744639248 0.14258123783953044 chr18 78077248 1293733 0.0165699103533977 0.21631546613294425 chr19 59128983 1035349 0.01751000858580639 0.18928964100829207 chr20 63025520 1053225 0.016711087826010797 0.13740773632232847 chr21 48129895 634327 0.013179480237802306 0.12555143601284174 chr22 51304566 594832 0.011594133746302424 0.11345128758023532 chrMT 16571 7415 0.4474684690121296 0.7187674975145845 chrX 155270560 3944293 0.02540270995351598 0.1736349002392061 chrY 59373566 164461 0.0027699363720211784 0.07731696159234958