BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717058.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 = 669,750 number of mapped reads = 600,794 (89.7%) number of supplementary alignments = 2,227 (0.33%) number of secondary alignments = 0 number of mapped bases = 34,151,064 bp number of sequenced bases = 34,140,228 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,468 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2653 >>>>>>> ACTG content number of A's = 7,857,265 bp (23.01%) number of C's = 6,551,970 bp (19.19%) number of T's = 11,425,274 bp (33.47%) number of G's = 8,305,025 bp (24.33%) number of N's = 694 bp (0%) GC percentage = 43.52% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 177,980 number of insertions = 2,750 mapped reads with insertion percentage = 0.46% number of deletions = 6,762 mapped reads with deletion percentage = 1.12% homopolymer indels = 39.84% >>>>>>> Coverage mean coverageData = 0.011X std coverageData = 0.1342X There is a 1.03% of reference with a coverageData >= 1X There is a 0.05% 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 2737861 0.010984369824298252 0.1778069120717718 chr2 243199373 2858092 0.011752053324578267 0.1844562601468488 chr3 198022430 2267642 0.011451440122212417 0.11261346972824729 chr4 191154276 2187438 0.01144331189326887 0.1252415566321273 chr5 180915260 2008806 0.0111035741263617 0.11066577086487313 chr6 171115067 1937234 0.011321235668861352 0.1174474093020057 chr7 159138663 1897018 0.011920534986523042 0.14958097088182237 chr8 146364022 1735611 0.011858180557514333 0.15077413063055542 chr9 141213431 1439516 0.010193902873162256 0.11934719465671376 chr10 135534747 1666807 0.012298005027448792 0.14778357790451171 chr11 135006516 1538133 0.011393027874299045 0.12375231173548111 chr12 133851895 1560314 0.011657018378409958 0.11461985889291972 chr13 115169878 1031888 0.00895970385589885 0.0998542411722145 chr14 107349540 1043486 0.009720451526853306 0.1043482102526312 chr15 102531392 1000371 0.009756728944048668 0.10469056942530255 chr16 90354753 1021449 0.011304872915761276 0.11621404561000033 chr17 81195210 951053 0.011713166330870996 0.11696583176961232 chr18 78077248 896250 0.01147901626860619 0.15883563192141828 chr19 59128983 758284 0.012824235451504384 0.1528887618073936 chr20 63025520 735206 0.0116652111716016 0.11477319529515632 chr21 48129895 454934 0.009452212600920903 0.11141882098720816 chr22 51304566 421440 0.008214473542179463 0.09562749913568869 chrMT 16571 5347 0.32267213807253636 0.6344997331848458 chrX 155270560 1866900 0.012023528478289768 0.1194708048824801 chrY 59373566 129984 0.0021892570845416293 0.09933826878965409