BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16362016.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 466,978,888 number of mapped reads = 447,856,148 (95.91%) number of supplementary alignments = 21,431,751 (4.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 225,117,761 number of mapped paired reads (second in pair) = 222,738,387 number of mapped paired reads (both in pair) = 444,514,948 number of mapped paired reads (singletons) = 3,341,200 number of mapped bases = 61,968,677,279 bp number of sequenced bases = 61,913,842,659 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,440,742 duplication rate = 34.13% >>>>>>> Insert size mean insert size = 136,241.5706 std insert size = 3,581,443.1307 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 53.8135 >>>>>>> ACTG content number of A's = 18,015,916,398 bp (29.1%) number of C's = 12,916,530,204 bp (20.86%) number of T's = 17,876,367,659 bp (28.87%) number of G's = 13,100,303,254 bp (21.16%) number of N's = 4,725,144 bp (0.01%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 526,349,137 number of insertions = 10,460,351 mapped reads with insertion percentage = 2.22% number of deletions = 31,078,944 mapped reads with deletion percentage = 6.65% homopolymer indels = 44.6% >>>>>>> Coverage mean coverageData = 20.0177X std coverageData = 233.8248X There is a 91.57% of reference with a coverageData >= 1X There is a 91.45% of reference with a coverageData >= 2X There is a 91.32% of reference with a coverageData >= 3X There is a 91.15% of reference with a coverageData >= 4X There is a 90.9% of reference with a coverageData >= 5X There is a 90.52% of reference with a coverageData >= 6X There is a 89.93% of reference with a coverageData >= 7X There is a 89.08% of reference with a coverageData >= 8X There is a 87.89% of reference with a coverageData >= 9X There is a 86.3% of reference with a coverageData >= 10X There is a 84.27% of reference with a coverageData >= 11X There is a 81.76% of reference with a coverageData >= 12X There is a 78.76% of reference with a coverageData >= 13X There is a 75.31% of reference with a coverageData >= 14X There is a 71.43% of reference with a coverageData >= 15X There is a 67.2% of reference with a coverageData >= 16X There is a 62.69% of reference with a coverageData >= 17X There is a 57.99% of reference with a coverageData >= 18X There is a 53.19% of reference with a coverageData >= 19X There is a 48.37% of reference with a coverageData >= 20X There is a 43.63% of reference with a coverageData >= 21X There is a 39.04% of reference with a coverageData >= 22X There is a 34.66% of reference with a coverageData >= 23X There is a 30.54% of reference with a coverageData >= 24X There is a 26.71% of reference with a coverageData >= 25X There is a 23.2% of reference with a coverageData >= 26X There is a 20.02% of reference with a coverageData >= 27X There is a 17.17% of reference with a coverageData >= 28X There is a 14.64% of reference with a coverageData >= 29X There is a 12.42% of reference with a coverageData >= 30X There is a 10.48% of reference with a coverageData >= 31X There is a 8.81% of reference with a coverageData >= 32X There is a 7.38% of reference with a coverageData >= 33X There is a 6.16% of reference with a coverageData >= 34X There is a 5.13% of reference with a coverageData >= 35X There is a 4.26% of reference with a coverageData >= 36X There is a 3.54% of reference with a coverageData >= 37X There is a 2.94% of reference with a coverageData >= 38X There is a 2.44% of reference with a coverageData >= 39X There is a 2.04% of reference with a coverageData >= 40X There is a 1.7% of reference with a coverageData >= 41X There is a 1.43% of reference with a coverageData >= 42X There is a 1.21% of reference with a coverageData >= 43X There is a 1.03% of reference with a coverageData >= 44X There is a 0.89% of reference with a coverageData >= 45X There is a 0.77% of reference with a coverageData >= 46X There is a 0.67% of reference with a coverageData >= 47X There is a 0.6% of reference with a coverageData >= 48X There is a 0.53% of reference with a coverageData >= 49X There is a 0.48% of reference with a coverageData >= 50X There is a 0.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5102076664 20.46966480376392 610.6797695088292 chr2 243199373 5274522825 21.68806095153872 140.9809722783223 chr3 198022430 4093339960 20.671092461596395 17.438819589041657 chr4 191154276 4044242448 21.15695517059739 132.28312322473226 chr5 180915260 3731706387 20.626819357305735 15.751878131114479 chr6 171115067 3551932548 20.757567467743797 76.71434088682469 chr7 159138663 3347292599 21.03381124296614 140.3091877847373 chr8 146364022 3095704223 21.15071846686476 421.85605510435397 chr9 141213431 2609582937 18.479707762358668 224.58289452528797 chr10 135534747 3086104313 22.769838593493667 317.732301398439 chr11 135006516 2789780770 20.66404535615155 81.18581962453356 chr12 133851895 2772888045 20.716091057209162 13.69221820724206 chr13 115169878 1968664744 17.09357323448758 12.30379210576496 chr14 107349540 1868268105 17.40359674573361 17.524150356716362 chr15 102531392 1765778579 17.221833670218775 12.942685715522652 chr16 90354753 1918962491 21.238091271191898 154.58711034423172 chr17 81195210 1719075074 21.17212424230444 104.56943017144019 chr18 78077248 1676777572 21.47587952895061 200.56905845919454 chr19 59128983 1224844023 20.714782511987394 319.52400234240633 chr20 63025520 1267511694 20.111086651883237 38.753051861298125 chr21 48129895 831915221 17.284791936487707 63.40159998723654 chr22 51304566 738895872 14.402146428838321 16.560069948528792 chrMT 16571 186415464 11249.499969826806 1934.181950006546 chrX 155270560 3132074816 20.171723577219016 41.080735942891764 chrY 59373566 170319905 2.8686150500039025 134.77851344079951