BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472751.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 = 13,238,298 number of mapped reads = 13,098,342 (98.94%) number of supplementary alignments = 48,287 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,580,382 number of mapped paired reads (second in pair) = 6,517,960 number of mapped paired reads (both in pair) = 13,008,598 number of mapped paired reads (singletons) = 89,744 number of mapped bases = 1,290,973,752 bp number of sequenced bases = 1,290,786,561 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,877,129 duplication rate = 46.12% >>>>>>> Insert size mean insert size = 22,654.6088 std insert size = 1,491,997.7854 median insert size = 257 >>>>>>> Mapping quality mean mapping quality = 55.2236 >>>>>>> ACTG content number of A's = 361,583,954 bp (28.01%) number of C's = 285,933,197 bp (22.15%) number of T's = 359,735,654 bp (27.87%) number of G's = 283,284,702 bp (21.95%) number of N's = 249,054 bp (0.02%) GC percentage = 44.1% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 8,586,904 number of insertions = 78,940 mapped reads with insertion percentage = 0.59% number of deletions = 76,335 mapped reads with deletion percentage = 0.58% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.417X std coverageData = 15.8644X There is a 3.62% of reference with a coverageData >= 1X There is a 1.56% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 123409288 0.4951212859766556 16.76375638569658 chr2 243199373 98903810 0.4066778987954052 17.038334774984598 chr3 198022430 167571578 0.8462252382217509 23.985967196554707 chr4 191154276 53954076 0.2822540888386928 11.713249325000405 chr5 180915260 89199014 0.4930430633656884 20.123340327498518 chr6 171115067 87474497 0.5112027744465074 13.211299936089064 chr7 159138663 45061120 0.2831563314064037 8.164859219596943 chr8 146364022 57748806 0.3945560200579894 18.99740177338055 chr9 141213431 62465591 0.4423487947120271 10.090306251473628 chr10 135534747 45627317 0.3366466386660241 32.43066838140988 chr11 135006516 50627405 0.3749997148285791 10.901218054543909 chr12 133851895 55517466 0.4147678745975169 11.213756860446518 chr13 115169878 33198771 0.28825914880277986 12.965835869739276 chr14 107349540 27245008 0.253797156466623 9.747773468298268 chr15 102531392 28623616 0.2791692909036093 9.15845599213416 chr16 90354753 42296143 0.46811198742361676 13.238129250482901 chr17 81195210 52508278 0.6466918183966763 15.06529325435045 chr18 78077248 24280340 0.31097842997745 11.56409214144188 chr19 59128983 31085814 0.5257288798625203 15.37723121593506 chr20 63025520 20520338 0.3255877619097788 12.608709437779707 chr21 48129895 5697540 0.11837840078396182 5.6412705082671115 chr22 51304566 9837624 0.1917494828822838 4.846786933511987 chrMT 16571 2327 0.14042604550117677 0.5837203978563883 chrX 155270560 76583263 0.4932246203014918 14.406417171611007 chrY 59373566 1534722 0.02584857375755399 0.9144482443316762