BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630861.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017516/SRP017516.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 = 62,626,116 number of mapped reads = 62,080,483 (99.13%) number of supplementary alignments = 302,579 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 31,213,628 number of mapped paired reads (second in pair) = 30,866,855 number of mapped paired reads (both in pair) = 61,715,308 number of mapped paired reads (singletons) = 365,175 number of mapped bases = 6,044,690,315 bp number of sequenced bases = 6,043,136,374 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,159,590 duplication rate = 18.41% >>>>>>> Insert size mean insert size = 206,152.9527 std insert size = 4,277,947.3286 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 53.2608 >>>>>>> ACTG content number of A's = 1,864,515,975 bp (30.85%) number of C's = 1,158,936,785 bp (19.18%) number of T's = 1,827,064,698 bp (30.23%) number of G's = 1,185,279,997 bp (19.61%) number of N's = 7,338,919 bp (0.12%) GC percentage = 38.79% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 50,045,635 number of insertions = 11,976,107 mapped reads with insertion percentage = 19.14% number of deletions = 854,996 mapped reads with deletion percentage = 1.35% homopolymer indels = 23.25% >>>>>>> Coverage mean coverageData = 1.9526X std coverageData = 6.605X There is a 32.26% of reference with a coverageData >= 1X There is a 23.02% of reference with a coverageData >= 2X There is a 17.15% of reference with a coverageData >= 3X There is a 13.6% of reference with a coverageData >= 4X There is a 11.09% of reference with a coverageData >= 5X There is a 9.27% of reference with a coverageData >= 6X There is a 7.88% of reference with a coverageData >= 7X There is a 6.79% of reference with a coverageData >= 8X There is a 5.91% of reference with a coverageData >= 9X There is a 5.2% of reference with a coverageData >= 10X There is a 4.6% of reference with a coverageData >= 11X There is a 4.1% of reference with a coverageData >= 12X There is a 3.68% of reference with a coverageData >= 13X There is a 3.32% of reference with a coverageData >= 14X There is a 3% of reference with a coverageData >= 15X There is a 2.73% of reference with a coverageData >= 16X There is a 2.49% of reference with a coverageData >= 17X There is a 2.28% of reference with a coverageData >= 18X There is a 2.09% of reference with a coverageData >= 19X There is a 1.92% of reference with a coverageData >= 20X There is a 1.77% of reference with a coverageData >= 21X There is a 1.64% of reference with a coverageData >= 22X There is a 1.52% of reference with a coverageData >= 23X There is a 1.41% of reference with a coverageData >= 24X There is a 1.32% of reference with a coverageData >= 25X There is a 1.23% of reference with a coverageData >= 26X There is a 1.14% of reference with a coverageData >= 27X There is a 1.07% of reference with a coverageData >= 28X There is a 1% of reference with a coverageData >= 29X There is a 0.94% of reference with a coverageData >= 30X There is a 0.88% of reference with a coverageData >= 31X There is a 0.83% of reference with a coverageData >= 32X There is a 0.78% of reference with a coverageData >= 33X There is a 0.74% of reference with a coverageData >= 34X There is a 0.69% of reference with a coverageData >= 35X There is a 0.66% of reference with a coverageData >= 36X There is a 0.62% of reference with a coverageData >= 37X There is a 0.59% of reference with a coverageData >= 38X There is a 0.56% of reference with a coverageData >= 39X There is a 0.53% of reference with a coverageData >= 40X There is a 0.5% of reference with a coverageData >= 41X There is a 0.47% of reference with a coverageData >= 42X There is a 0.45% of reference with a coverageData >= 43X There is a 0.43% of reference with a coverageData >= 44X There is a 0.41% of reference with a coverageData >= 45X There is a 0.39% of reference with a coverageData >= 46X There is a 0.37% of reference with a coverageData >= 47X There is a 0.35% of reference with a coverageData >= 48X There is a 0.34% of reference with a coverageData >= 49X There is a 0.32% of reference with a coverageData >= 50X There is a 0.31% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 514453181 2.0639995958124415 6.923040867486739 chr2 243199373 527202101 2.1677773856760725 6.702733150661583 chr3 198022430 473781368 2.3925641554848105 8.251313841568217 chr4 191154276 442038133 2.312467930353805 6.288272775743624 chr5 180915260 404556000 2.2361629416998876 6.833668618600233 chr6 171115067 411024724 2.402037010569034 7.723975107794933 chr7 159138663 308117775 1.936159128093215 5.90003161600866 chr8 146364022 319409641 2.1822961451551257 6.366520865855621 chr9 141213431 223270455 1.5810851235531556 5.267929424271019 chr10 135534747 256495496 1.8924703935884426 6.405379321170858 chr11 135006516 284073431 2.1041460769197244 6.347118173648272 chr12 133851895 278564301 2.081138268531798 6.922298924351495 chr13 115169878 187343107 1.6266675822996008 4.811499747311294 chr14 107349540 174700298 1.6273968011413928 5.7604679762021025 chr15 102531392 157671301 1.5377856276446535 6.363657642846879 chr16 90354753 99523128 1.1014708656223098 3.8648600257607217 chr17 81195210 84376288 1.0391781485631972 3.8266998182479415 chr18 78077248 178212890 2.282520126733975 7.328496273409441 chr19 59128983 42939320 0.7261975062212722 3.7936306432082363 chr20 63025520 78854446 1.2511510575398663 4.653869104971302 chr21 48129895 53044118 1.102103339307098 3.6625286975040443 chr22 51304566 35123727 0.6846121064546185 4.020250783859909 chrMT 16571 1286 0.07760545531349948 0.38232314149048097 chrX 155270560 504988055 3.2523103864634737 10.698647692329025 chrY 59373566 4925745 0.08296191945082093 0.924077079185264