BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716898.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 = 1,077,144 number of mapped reads = 964,311 (89.52%) number of supplementary alignments = 21,401 (1.99%) number of secondary alignments = 0 number of mapped bases = 72,505,975 bp number of sequenced bases = 72,480,247 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,078 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2949 >>>>>>> ACTG content number of A's = 19,062,358 bp (26.3%) number of C's = 15,137,276 bp (20.88%) number of T's = 21,475,089 bp (29.63%) number of G's = 16,796,717 bp (23.17%) number of N's = 8,807 bp (0.01%) GC percentage = 44.06% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 544,332 number of insertions = 5,784 mapped reads with insertion percentage = 0.59% number of deletions = 15,195 mapped reads with deletion percentage = 1.56% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.0234X std coverageData = 0.2161X There is a 2.13% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5727096 0.022977258700591162 0.24610748761501888 chr2 243199373 6197965 0.025485119157770197 0.29738188705124935 chr3 198022430 4884782 0.02466782172100403 0.16793211937070254 chr4 191154276 4664423 0.024401353177158327 0.17561761660585207 chr5 180915260 4371547 0.024163506163051143 0.16808209207571853 chr6 171115067 4233522 0.024740790359507034 0.18345910339634666 chr7 159138663 3986608 0.02505115931506852 0.2698002013402729 chr8 146364022 3703292 0.025301928365975074 0.25890321132495464 chr9 141213431 3065198 0.021706136436837938 0.2250611734210663 chr10 135534747 3445576 0.025422086042629348 0.21331659072748113 chr11 135006516 3287212 0.024348543295495455 0.23032303056137504 chr12 133851895 3281662 0.024517112738672846 0.16965425754190352 chr13 115169878 2332628 0.020253802821602364 0.15188572633168054 chr14 107349540 2183629 0.02034129815553937 0.17546609232302288 chr15 102531392 2069587 0.020184910783226272 0.15209117579578246 chr16 90354753 2139652 0.023680569410665094 0.17503409801581946 chr17 81195210 1938634 0.023876211416905012 0.17900545842376112 chr18 78077248 1992008 0.025513296780132415 0.3925865918770233 chr19 59128983 1455859 0.024621749371200922 0.22917638033603038 chr20 63025520 1522081 0.02415023311192038 0.1714747313100139 chr21 48129895 933022 0.019385498347752474 0.15706631163757284 chr22 51304566 832800 0.016232473343600645 0.13666010929358055 chrMT 16571 4085 0.24651499607748475 0.48475561431883457 chrX 155270560 4082930 0.026295583657326926 0.20583323589867322 chrY 59373566 170177 0.0028662081708213383 0.08734695299906327