BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926898.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 33,409,418 number of mapped reads = 31,318,145 (93.74%) number of supplementary alignments = 175,460 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,736,141 number of mapped paired reads (second in pair) = 15,582,004 number of mapped paired reads (both in pair) = 31,025,884 number of mapped paired reads (singletons) = 292,261 number of mapped bases = 2,949,399,954 bp number of sequenced bases = 2,947,141,138 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,228,227 duplication rate = 5.56% >>>>>>> Insert size mean insert size = 81,387.5028 std insert size = 2,811,854.5643 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 53.6438 >>>>>>> ACTG content number of A's = 838,033,391 bp (28.44%) number of C's = 590,632,014 bp (20.04%) number of T's = 842,915,979 bp (28.6%) number of G's = 675,278,741 bp (22.91%) number of N's = 281,013 bp (0.01%) GC percentage = 42.95% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 30,592,927 number of insertions = 464,805 mapped reads with insertion percentage = 1.46% number of deletions = 1,608,568 mapped reads with deletion percentage = 5% homopolymer indels = 53.17% >>>>>>> Coverage mean coverageData = 0.9527X std coverageData = 3.8194X There is a 34.82% of reference with a coverageData >= 1X There is a 19.8% of reference with a coverageData >= 2X There is a 12.23% of reference with a coverageData >= 3X There is a 7.98% of reference with a coverageData >= 4X There is a 5.4% of reference with a coverageData >= 5X There is a 3.75% of reference with a coverageData >= 6X There is a 2.65% of reference with a coverageData >= 7X There is a 1.9% of reference with a coverageData >= 8X There is a 1.38% of reference with a coverageData >= 9X There is a 1.01% of reference with a coverageData >= 10X There is a 0.75% of reference with a coverageData >= 11X There is a 0.56% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 245283769 0.9840848861917179 3.6166530383231783 chr2 243199373 258636231 1.0634740863414973 4.431097764281818 chr3 198022430 196757401 0.9936116883324783 2.059445819260457 chr4 191154276 172579481 0.902828252714577 2.154724959224858 chr5 180915260 180554441 0.9980055911259227 2.018670705940627 chr6 171115067 170274773 0.9950893044386325 2.568241832276685 chr7 159138663 149955943 0.9422973661655056 2.2134416763024785 chr8 146364022 154012687 1.0522578219393288 2.230656316403042 chr9 141213431 128908786 0.9128649101373367 3.196935748571304 chr10 135534747 150898057 1.1133532938236126 12.910698300635113 chr11 135006516 144424350 1.0697583663295185 2.5600994094561185 chr12 133851895 117296886 0.876318456305755 1.9904950625359505 chr13 115169878 89959294 0.7811008882027295 1.7852931464541426 chr14 107349540 90044082 0.8387933660451642 1.914161677671198 chr15 102531392 91667237 0.89404069536089 2.0635539841001016 chr16 90354753 96717663 1.0704214198892226 4.549134570349724 chr17 81195210 79818797 0.9830481009901939 2.353394987512202 chr18 78077248 79939032 1.0238454101251109 3.2498438437210293 chr19 59128983 50837595 0.8597745542148086 2.4594509307828494 chr20 63025520 65606326 1.0409485871754807 2.328902946492024 chr21 48129895 37752065 0.7843787109861761 2.775762319625893 chr22 51304566 38844047 0.7571265099484518 1.9884080497818373 chrMT 16571 17706 1.0684931506849316 1.3951065554166289 chrX 155270560 154198474 0.9930953684974151 2.131079560106323 chrY 59373566 4414831 0.07435684425624696 1.759458350254387