BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960905.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 156,845,918 number of mapped reads = 153,717,147 (98.01%) number of supplementary alignments = 314,641 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 77,188,369 number of mapped paired reads (second in pair) = 76,528,778 number of mapped paired reads (both in pair) = 152,561,020 number of mapped paired reads (singletons) = 1,156,127 number of mapped bases = 15,137,843,776 bp number of sequenced bases = 15,133,405,441 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,015,824 duplication rate = 5.13% >>>>>>> Insert size mean insert size = 20,257.8748 std insert size = 1,335,004.355 median insert size = 150 >>>>>>> Mapping quality mean mapping quality = 53.6393 >>>>>>> ACTG content number of A's = 4,473,858,561 bp (29.56%) number of C's = 3,083,193,047 bp (20.37%) number of T's = 4,461,628,182 bp (29.48%) number of G's = 3,107,263,403 bp (20.53%) number of N's = 7,462,248 bp (0.05%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 148,160,518 number of insertions = 1,698,125 mapped reads with insertion percentage = 1.07% number of deletions = 1,855,807 mapped reads with deletion percentage = 1.17% homopolymer indels = 40.92% >>>>>>> Coverage mean coverageData = 4.89X std coverageData = 51.8266X There is a 88.92% of reference with a coverageData >= 1X There is a 83.16% of reference with a coverageData >= 2X There is a 73.68% of reference with a coverageData >= 3X There is a 61.79% of reference with a coverageData >= 4X There is a 48.89% of reference with a coverageData >= 5X There is a 36.64% of reference with a coverageData >= 6X There is a 26.08% of reference with a coverageData >= 7X There is a 17.72% of reference with a coverageData >= 8X There is a 11.55% of reference with a coverageData >= 9X There is a 7.27% of reference with a coverageData >= 10X There is a 4.45% of reference with a coverageData >= 11X There is a 2.68% of reference with a coverageData >= 12X There is a 1.61% of reference with a coverageData >= 13X There is a 0.98% of reference with a coverageData >= 14X There is a 0.62% of reference with a coverageData >= 15X There is a 0.42% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.2% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.09% of reference with a coverageData >= 29X There is a 0.08% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1232932603 4.946557798144864 129.16791840628306 chr2 243199373 1301657097 5.352222256757217 32.8404503444313 chr3 198022430 1004723293 5.073785292908485 9.084426088399292 chr4 191154276 1022321585 5.348149182914433 40.14320623554207 chr5 180915260 916099370 5.063693189839265 5.375886574139708 chr6 171115067 872652337 5.099798353817668 15.925676660762239 chr7 159138663 809705246 5.088048565545634 33.28692482735062 chr8 146364022 766268347 5.23536000534339 57.79330010919756 chr9 141213431 631743147 4.473676069806703 46.01751412176852 chr10 135534747 776865122 5.731852083657928 108.7566623270615 chr11 135006516 682272886 5.053629307788373 21.360610447843207 chr12 133851895 669370860 5.000832151087589 4.526567107167959 chr13 115169878 486187177 4.221478614399505 3.449076023173554 chr14 107349540 447357673 4.1672993941101195 4.8995125344818256 chr15 102531392 419318297 4.089657702101616 3.51803983918447 chr16 90354753 468630196 5.186558320844505 43.42197616641797 chr17 81195210 397318631 4.893375249599083 20.042507621147358 chr18 78077248 414895730 5.313913343871956 55.5120300953041 chr19 59128983 286252011 4.841145517419097 62.956680176140274 chr20 63025520 308829105 4.900064370750134 15.795569210956142 chr21 48129895 207253742 4.306133267068212 21.074237575514665 chr22 51304566 172430210 3.360913529606702 4.328694738903599 chrMT 16571 11562023 697.7263291292016 103.80485472046747 chrX 155270560 783646129 5.046971744031837 16.596007684421796 chrY 59373566 47550959 0.8008775993006719 44.156894147858225