BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472459.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,684,186 number of mapped reads = 17,524,810 (99.1%) number of supplementary alignments = 62,749 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,778,246 number of mapped paired reads (second in pair) = 8,746,564 number of mapped paired reads (both in pair) = 17,441,432 number of mapped paired reads (singletons) = 83,378 number of mapped bases = 1,714,495,866 bp number of sequenced bases = 1,714,270,335 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,078,497 duplication rate = 48.12% >>>>>>> Insert size mean insert size = 18,413.2222 std insert size = 1,350,543.6611 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 55.1439 >>>>>>> ACTG content number of A's = 462,335,921 bp (26.97%) number of C's = 396,070,205 bp (23.1%) number of T's = 462,026,354 bp (26.95%) number of G's = 393,616,115 bp (22.96%) number of N's = 221,740 bp (0.01%) GC percentage = 46.07% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 9,237,486 number of insertions = 99,609 mapped reads with insertion percentage = 0.56% number of deletions = 87,426 mapped reads with deletion percentage = 0.49% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.5538X std coverageData = 17.4866X There is a 4.62% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187940950 0.7540239990013906 24.31384237124211 chr2 243199373 132762921 0.5459015759880269 17.381643651203124 chr3 198022430 154531884 0.7803756574444622 17.009933776391836 chr4 191154276 78075113 0.4084403165535256 19.593088983371874 chr5 180915260 70594226 0.3902060334766675 13.375004046842346 chr6 171115067 132985870 0.7771721820381837 21.20309325734587 chr7 159138663 83979135 0.5277104470834972 16.68743572538615 chr8 146364022 94327316 0.6444706473015616 17.87329045091552 chr9 141213431 96137126 0.6807930755538402 18.65547710847715 chr10 135534747 44373534 0.32739599978741984 11.286643227193556 chr11 135006516 70335005 0.5209748913156163 16.091047951434255 chr12 133851895 87698418 0.6551899620098767 16.866326455594326 chr13 115169878 43186963 0.37498488102939553 13.876983989976047 chr14 107349540 53895143 0.5020528546279751 20.25569312811115 chr15 102531392 48213147 0.47022815217411656 15.24550365507602 chr16 90354753 73000438 0.8079313547567332 21.072509315915045 chr17 81195210 67432400 0.830497267018584 23.314861013040954 chr18 78077248 27770704 0.3556824133965377 12.91512584292713 chr19 59128983 48593227 0.8218173987535013 18.947188088795244 chr20 63025520 32783865 0.5201681001600621 16.233598628512134 chr21 48129895 9735405 0.20227355575988687 11.978887933690077 chr22 51304566 18849425 0.36740248421553745 10.034999524495976 chrMT 16571 2570 0.15509021785046165 0.4974995191315022 chrX 155270560 54396510 0.3503337013790637 10.588228737577232 chrY 59373566 2894571 0.04875184690776364 3.003772603002593