BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617666.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,666,374 (95.83%) number of supplementary alignments = 140,964 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,388,784 number of mapped paired reads (second in pair) = 15,277,590 number of mapped paired reads (both in pair) = 30,142,080 number of mapped paired reads (singletons) = 524,294 number of mapped bases = 2,988,346,979 bp number of sequenced bases = 2,986,527,271 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,165,414 duplication rate = 10.89% >>>>>>> Insert size mean insert size = 31,354.2652 std insert size = 1,610,718.7665 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 52.7294 >>>>>>> ACTG content number of A's = 888,046,157 bp (29.74%) number of C's = 596,259,965 bp (19.96%) number of T's = 887,375,161 bp (29.71%) number of G's = 612,630,016 bp (20.51%) number of N's = 2,215,972 bp (0.07%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 41,467,800 number of insertions = 464,386 mapped reads with insertion percentage = 1.49% number of deletions = 1,098,558 mapped reads with deletion percentage = 3.51% homopolymer indels = 47.78% >>>>>>> Coverage mean coverageData = 0.9653X std coverageData = 10.8674X There is a 33.57% of reference with a coverageData >= 1X There is a 19.55% of reference with a coverageData >= 2X There is a 12.01% of reference with a coverageData >= 3X There is a 7.71% of reference with a coverageData >= 4X There is a 5.09% of reference with a coverageData >= 5X There is a 3.46% of reference with a coverageData >= 6X There is a 2.41% of reference with a coverageData >= 7X There is a 1.72% of reference with a coverageData >= 8X There is a 1.24% of reference with a coverageData >= 9X There is a 0.92% of reference with a coverageData >= 10X There is a 0.69% of reference with a coverageData >= 11X There is a 0.53% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 183324583 0.7355030140526712 10.382687429853167 chr2 243199373 309013413 1.270617638475573 12.508168713443949 chr3 198022430 249970569 1.2623346203760857 2.4966844423244496 chr4 191154276 167071740 0.8740151855143434 8.763264199620838 chr5 180915260 197808928 1.0933789001546912 2.3726825148202075 chr6 171115067 144805683 0.8462474143203298 5.903873189097354 chr7 159138663 234016041 1.4705165708222645 13.780089115759786 chr8 146364022 132831149 0.9075396206316331 4.154300026431915 chr9 141213431 122515923 0.867593982614869 20.961429737527794 chr10 135534747 126599898 0.934077059958654 22.03551983478289 chr11 135006516 164468896 1.2182293186500717 12.248478568734482 chr12 133851895 127459159 0.9522402279026382 2.174030739193515 chr13 115169878 128378161 1.1146852217730057 2.324063019762059 chr14 107349540 85449253 0.7959908631187428 2.498691851397467 chr15 102531392 63696119 0.6212352895784347 1.5890603427240537 chr16 90354753 82740635 0.9157308525872457 17.046470116605708 chr17 81195210 73917099 0.9103628034215319 13.09726251335986 chr18 78077248 55192960 0.70690196457744 18.59568743867507 chr19 59128983 31678289 0.5357489236708164 6.197758182255363 chr20 63025520 80932321 1.2841198454213467 3.111866519793455 chr21 48129895 43663940 0.9072103730955573 4.533403180469372 chr22 51304566 19209671 0.37442419842319685 1.2792741061568438 chrMT 16571 3111765 187.7837788908334 130.44610208416728 chrX 155270560 148399094 0.9557452101673363 4.438527642114636 chrY 59373566 12091690 0.20365443436562325 18.116089164792523