BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716131.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 = 1,244,770 number of mapped reads = 1,131,657 (90.91%) number of supplementary alignments = 23,366 (1.88%) number of secondary alignments = 0 number of mapped bases = 88,949,510 bp number of sequenced bases = 88,910,386 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,082 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2127 >>>>>>> ACTG content number of A's = 23,378,868 bp (26.29%) number of C's = 17,357,347 bp (19.52%) number of T's = 27,394,096 bp (30.81%) number of G's = 20,774,056 bp (23.37%) number of N's = 6,019 bp (0.01%) GC percentage = 42.89% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 592,479 number of insertions = 7,785 mapped reads with insertion percentage = 0.68% number of deletions = 20,107 mapped reads with deletion percentage = 1.75% homopolymer indels = 42.47% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.2863X There is a 2.56% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 8664578 0.03476251318948569 0.5670356424132068 chr2 243199373 7412673 0.030479819534732108 0.30753588698391726 chr3 198022430 5565576 0.028105785794063833 0.18098355964617577 chr4 191154276 5301605 0.027734692160378355 0.2229560173052093 chr5 180915260 4889824 0.027028256212328357 0.17860043992566876 chr6 171115067 4852026 0.028355340561564926 0.19264231123992506 chr7 159138663 4720309 0.02966161026500518 0.3260902441537624 chr8 146364022 4447714 0.030388028008686452 0.3237342467080946 chr9 141213431 3652776 0.025867057928788656 0.2467525226508182 chr10 135534747 4169566 0.030763815864871907 0.29502017275387055 chr11 135006516 4969178 0.03680694937716932 0.3009218087117926 chr12 133851895 3877904 0.028971603278384665 0.184356480849478 chr13 115169878 3204146 0.027821041887358778 0.18196658041052063 chr14 107349540 2667178 0.024845732920699987 0.1815025379470984 chr15 102531392 2543955 0.024811474323883167 0.17058902702599346 chr16 90354753 2036617 0.022540230949444354 0.17594621946291503 chr17 81195210 2745789 0.03381713034549698 0.22750366579488157 chr18 78077248 2345450 0.030040121291160262 0.3955693696316214 chr19 59128983 1728481 0.02923238169004192 0.3864400723765408 chr20 63025520 1863961 0.029574702437996547 0.19482910761559885 chr21 48129895 1141208 0.023711001239458344 0.19447646583449177 chr22 51304566 1000174 0.019494834046544708 0.15191871359113493 chrMT 16571 7867 0.4747450365095649 0.7556489847802358 chrX 155270560 4857285 0.03128271708429466 0.2153335813911167 chrY 59373566 283670 0.0047777153893704145 0.18276696615757493