BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054601.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,500,766 number of mapped reads = 6,459,692 (75.99%) number of supplementary alignments = 222 (0%) number of secondary alignments = 0 number of mapped bases = 304,230,267 bp number of sequenced bases = 304,164,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,305,946 duplication rate = 15.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.898 >>>>>>> ACTG content number of A's = 93,486,546 bp (30.74%) number of C's = 56,506,696 bp (18.58%) number of T's = 93,670,236 bp (30.8%) number of G's = 60,418,023 bp (19.86%) number of N's = 82,600 bp (0.03%) GC percentage = 38.44% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,757,767 number of insertions = 13,894 mapped reads with insertion percentage = 0.21% number of deletions = 45,799 mapped reads with deletion percentage = 0.71% homopolymer indels = 48.82% >>>>>>> Coverage mean coverageData = 0.0983X std coverageData = 0.7316X There is a 4.84% of reference with a coverageData >= 1X There is a 1.85% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 28186173 0.1130836620864427 0.8269134504808772 chr2 243199373 27615949 0.1135527146280924 0.8549899822387317 chr3 198022430 22818496 0.1152318755001643 0.7514957219395586 chr4 191154276 18439640 0.09646470058561495 0.6850422383815593 chr5 180915260 15116502 0.08355570447733375 0.5921928103985131 chr6 171115067 14927362 0.0872358130800954 0.6779510167876536 chr7 159138663 19907550 0.12509562179745096 0.9496917924937811 chr8 146364022 15952868 0.1089944631338431 0.779945596817521 chr9 141213431 14995743 0.10619204486292809 0.7522055069121513 chr10 135534747 12829294 0.09465686315849323 0.7091002302147049 chr11 135006516 13349163 0.09887791638145821 0.7065155810022223 chr12 133851895 10893539 0.08138501886730853 0.5943040425085583 chr13 115169878 9323217 0.08095187007144351 0.5926065104078031 chr14 107349540 6124831 0.057055027902308666 0.5416318903460356 chr15 102531392 5769952 0.056274979666715144 0.47564124191517027 chr16 90354753 7784528 0.08615515777017287 0.6371111257491667 chr17 81195210 5449242 0.06711285062259215 0.5337587195852195 chr18 78077248 11920693 0.15267819121903478 0.9334042750600398 chr19 59128983 5127771 0.08672178582878722 0.6916093939821967 chr20 63025520 5456798 0.08658076918683098 0.6259399585572585 chr21 48129895 3393483 0.07050676092270719 0.6192950557061833 chr22 51304566 2654445 0.051738962181260825 0.45120212832724166 chrMT 16571 50733 3.0615533160340354 6.944054973749314 chrX 155270560 25426791 0.163757965450759 1.0093907024292441 chrY 59373566 715504 0.012050884732104519 0.23506690636309868