BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524509.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 = 6,104,378 number of mapped reads = 5,626,195 (92.17%) number of supplementary alignments = 25,833 (0.42%) number of secondary alignments = 0 number of mapped bases = 330,489,459 bp number of sequenced bases = 330,393,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 635,308 duplication rate = 8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8144 >>>>>>> ACTG content number of A's = 84,691,696 bp (25.63%) number of C's = 68,731,400 bp (20.8%) number of T's = 98,687,515 bp (29.87%) number of G's = 78,278,312 bp (23.69%) number of N's = 5,058 bp (0%) GC percentage = 44.5% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,645,672 number of insertions = 20,134 mapped reads with insertion percentage = 0.36% number of deletions = 56,483 mapped reads with deletion percentage = 1% homopolymer indels = 43.9% >>>>>>> Coverage mean coverageData = 0.1068X std coverageData = 0.8419X There is a 7.26% of reference with a coverageData >= 1X There is a 2.04% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 31976408 0.1282901838788197 1.6920577766930185 chr2 243199373 26039481 0.10707051041615967 1.0556283735129401 chr3 198022430 17205193 0.08688507155477286 0.4191166936069203 chr4 191154276 18984196 0.09931347808301186 0.6218568927078085 chr5 180915260 18281420 0.10104962953373861 0.44517584485807 chr6 171115067 13988435 0.081748704221353 0.5747163222910742 chr7 159138663 15870793 0.0997293347877379 1.025446412493429 chr8 146364022 29706757 0.20296488572854332 0.8337512443342429 chr9 141213431 14815661 0.10491679789297095 0.6557438261272258 chr10 135534747 17659143 0.13029236701935926 0.9704128066377962 chr11 135006516 12166360 0.09011683554592284 0.6927554818084071 chr12 133851895 14081437 0.10520162602105858 0.4590743761256412 chr13 115169878 7570392 0.06573239575716143 0.3604880607650362 chr14 107349540 7809848 0.07275157397041478 0.4019223469145477 chr15 102531392 8709241 0.08494219019283382 0.41742858938892297 chr16 90354753 10937481 0.12105042221741229 0.5643109996594633 chr17 81195210 12060837 0.14854123783903017 0.6224525870800639 chr18 78077248 7836236 0.10036516655914922 1.3578525023981958 chr19 59128983 7305270 0.12354804072987353 1.1815985889298948 chr20 63025520 9661079 0.1532883663633398 0.5910835714460118 chr21 48129895 4823850 0.100225649775467 0.5813667077546816 chr22 51304566 2859307 0.05573201808197734 0.3342489115546489 chrMT 16571 51752 3.123046285679802 2.6479183192859375 chrX 155270560 18843213 0.12135728112270606 0.5670793154472102 chrY 59373566 1245669 0.020980195125891547 0.6357589075498292