BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716375.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 = 2,321,458 number of mapped reads = 2,119,778 (91.31%) number of supplementary alignments = 46,119 (1.99%) number of secondary alignments = 0 number of mapped bases = 165,834,712 bp number of sequenced bases = 165,760,675 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,013 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2192 >>>>>>> ACTG content number of A's = 43,415,752 bp (26.19%) number of C's = 32,903,507 bp (19.85%) number of T's = 50,445,220 bp (30.43%) number of G's = 38,985,039 bp (23.52%) number of N's = 11,157 bp (0.01%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,126,252 number of insertions = 13,462 mapped reads with insertion percentage = 0.63% number of deletions = 39,342 mapped reads with deletion percentage = 1.83% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.0536X std coverageData = 0.4437X There is a 4.55% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13269004 0.053235590534396304 0.8253180489380807 chr2 243199373 14100606 0.05797961493922108 0.5237454009861672 chr3 198022430 10743890 0.054255924442498764 0.2629712448694461 chr4 191154276 10810915 0.056555967390444356 0.3356064961951063 chr5 180915260 9980303 0.055165622844640085 0.2698918429806281 chr6 171115067 9684014 0.056593578635597296 0.30544079467940416 chr7 159138663 9207014 0.057855293153996144 0.5854218296101817 chr8 146364022 8513067 0.05816365855264622 0.5599697870338662 chr9 141213431 6749328 0.04779522707015029 0.3997000708008911 chr10 135534747 8042873 0.059341778975689534 0.4602918021258667 chr11 135006516 7637777 0.056573395316711975 0.427005443618939 chr12 133851895 7586906 0.056681349188220306 0.2731846781283965 chr13 115169878 5239177 0.0454908617685607 0.2403763135316248 chr14 107349540 4880568 0.04546426561306178 0.2612727746614446 chr15 102531392 4749841 0.046325724320606124 0.2457643371656818 chr16 90354753 4825613 0.0534074062490105 0.2894535173146579 chr17 81195210 4499197 0.05541209881715929 0.314079136600177 chr18 78077248 4303348 0.05511654304209083 0.6447954412653579 chr19 59128983 3264383 0.05520783267995663 0.6003732438818812 chr20 63025520 3578327 0.056775842547590244 0.28465999782258106 chr21 48129895 2244149 0.04662692490810545 0.28581254382428234 chr22 51304566 1913622 0.037299253247751865 0.21983255221735765 chrMT 16571 16130 0.97338724277352 1.177559166898489 chrX 155270560 9499506 0.06118034223615861 0.33090296972733846 chrY 59373566 495154 0.00833963720488003 0.26100504618121223