BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504413.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 142,220,378 number of mapped reads = 135,374,488 (95.19%) number of supplementary alignments = 2,201,462 (1.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 67,755,584 number of mapped paired reads (second in pair) = 67,618,904 number of mapped paired reads (both in pair) = 134,987,664 number of mapped paired reads (singletons) = 386,824 number of mapped bases = 12,978,552,476 bp number of sequenced bases = 12,974,334,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,953,035 duplication rate = 28.66% >>>>>>> Insert size mean insert size = 75,295.1774 std insert size = 2,622,633.7245 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 50.5561 >>>>>>> ACTG content number of A's = 3,857,785,229 bp (29.73%) number of C's = 2,621,360,406 bp (20.2%) number of T's = 3,853,961,384 bp (29.7%) number of G's = 2,631,299,411 bp (20.28%) number of N's = 9,928,360 bp (0.08%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 66,090,974 number of insertions = 1,197,109 mapped reads with insertion percentage = 0.88% number of deletions = 2,498,112 mapped reads with deletion percentage = 1.82% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 4.1925X std coverageData = 49.2288X There is a 28.18% of reference with a coverageData >= 1X There is a 21.76% of reference with a coverageData >= 2X There is a 17.04% of reference with a coverageData >= 3X There is a 14.4% of reference with a coverageData >= 4X There is a 12.37% of reference with a coverageData >= 5X There is a 10.9% of reference with a coverageData >= 6X There is a 9.72% of reference with a coverageData >= 7X There is a 8.77% of reference with a coverageData >= 8X There is a 7.99% of reference with a coverageData >= 9X There is a 7.33% of reference with a coverageData >= 10X There is a 6.77% of reference with a coverageData >= 11X There is a 6.28% of reference with a coverageData >= 12X There is a 5.86% of reference with a coverageData >= 13X There is a 5.48% of reference with a coverageData >= 14X There is a 5.15% of reference with a coverageData >= 15X There is a 4.86% of reference with a coverageData >= 16X There is a 4.59% of reference with a coverageData >= 17X There is a 4.35% of reference with a coverageData >= 18X There is a 4.13% of reference with a coverageData >= 19X There is a 3.93% of reference with a coverageData >= 20X There is a 3.75% of reference with a coverageData >= 21X There is a 3.58% of reference with a coverageData >= 22X There is a 3.43% of reference with a coverageData >= 23X There is a 3.28% of reference with a coverageData >= 24X There is a 3.15% of reference with a coverageData >= 25X There is a 3.02% of reference with a coverageData >= 26X There is a 2.91% of reference with a coverageData >= 27X There is a 2.8% of reference with a coverageData >= 28X There is a 2.7% of reference with a coverageData >= 29X There is a 2.6% of reference with a coverageData >= 30X There is a 2.51% of reference with a coverageData >= 31X There is a 2.43% of reference with a coverageData >= 32X There is a 2.35% of reference with a coverageData >= 33X There is a 2.28% of reference with a coverageData >= 34X There is a 2.2% of reference with a coverageData >= 35X There is a 2.14% of reference with a coverageData >= 36X There is a 2.07% of reference with a coverageData >= 37X There is a 2.01% of reference with a coverageData >= 38X There is a 1.95% of reference with a coverageData >= 39X There is a 1.9% of reference with a coverageData >= 40X There is a 1.85% of reference with a coverageData >= 41X There is a 1.8% of reference with a coverageData >= 42X There is a 1.75% of reference with a coverageData >= 43X There is a 1.7% of reference with a coverageData >= 44X There is a 1.66% of reference with a coverageData >= 45X There is a 1.62% of reference with a coverageData >= 46X There is a 1.58% of reference with a coverageData >= 47X There is a 1.54% of reference with a coverageData >= 48X There is a 1.5% of reference with a coverageData >= 49X There is a 1.47% of reference with a coverageData >= 50X There is a 1.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1294747104 5.194559190285829 89.97961717577691 chr2 243199373 1105898859 4.547293216089007 25.978141640797904 chr3 198022430 881619856 4.452121186473674 23.357313088943876 chr4 191154276 822140458 4.300926326126233 25.284942335569923 chr5 180915260 875413330 4.838803150159914 39.85827208828591 chr6 171115067 828789459 4.843462785191207 38.69983756503793 chr7 159138663 983251877 6.178585759514644 88.5373646031465 chr8 146364022 884322147 6.041936637953281 81.99490390612415 chr9 141213431 497309883 3.5216896826194954 22.629251707898742 chr10 135534747 579263119 4.2739085867036 40.306522270094675 chr11 135006516 679665435 5.034315788135737 37.34761124018644 chr12 133851895 683572619 5.106932696021973 64.02787211928134 chr13 115169878 427314541 3.7102977655320606 46.78525009993642 chr14 107349540 432917743 4.032786195450861 51.565975369315815 chr15 102531392 381615346 3.7219366533129676 57.74118990591505 chr16 90354753 307111036 3.398947214210192 40.34183298696496 chr17 81195210 199563395 2.4578222656237974 15.864002125630467 chr18 78077248 353402476 4.526318294415295 36.472190522835774 chr19 59128983 110693545 1.8720691509272196 11.246537145984412 chr20 63025520 207896471 3.298607786179313 23.96661303272189 chr21 48129895 155380806 3.228363702019296 24.52123419093248 chr22 51304566 98772364 1.9252158570057878 16.14118519048815 chrMT 16571 576 0.034759519642749384 0.30445156583641275 chrX 155270560 21944042 0.14132777005505745 1.9403420217294491 chrY 59373566 165945989 2.7949473171276256 26.71456756043789