BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960893.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 = 223,815,558 number of mapped reads = 220,235,827 (98.4%) number of supplementary alignments = 391,831 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 110,340,527 number of mapped paired reads (second in pair) = 109,895,300 number of mapped paired reads (both in pair) = 219,055,414 number of mapped paired reads (singletons) = 1,180,413 number of mapped bases = 21,668,114,025 bp number of sequenced bases = 21,661,779,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,847,738 duplication rate = 9.78% >>>>>>> Insert size mean insert size = 15,557.1949 std insert size = 1,176,638.5155 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 53.6355 >>>>>>> ACTG content number of A's = 6,616,268,600 bp (30.54%) number of C's = 4,220,641,142 bp (19.48%) number of T's = 6,603,872,150 bp (30.49%) number of G's = 4,220,217,939 bp (19.48%) number of N's = 779,312 bp (0%) GC percentage = 38.97% >>>>>>> Mismatches and indels general error rate = 0.012 number of mismatches = 253,286,904 number of insertions = 2,586,551 mapped reads with insertion percentage = 1.14% number of deletions = 2,722,929 mapped reads with deletion percentage = 1.2% homopolymer indels = 40.78% >>>>>>> Coverage mean coverageData = 6.9994X std coverageData = 94.875X There is a 89.42% of reference with a coverageData >= 1X There is a 85.28% of reference with a coverageData >= 2X There is a 79.12% of reference with a coverageData >= 3X There is a 71.51% of reference with a coverageData >= 4X There is a 63.01% of reference with a coverageData >= 5X There is a 54.27% of reference with a coverageData >= 6X There is a 45.77% of reference with a coverageData >= 7X There is a 37.89% of reference with a coverageData >= 8X There is a 30.84% of reference with a coverageData >= 9X There is a 24.7% of reference with a coverageData >= 10X There is a 19.5% of reference with a coverageData >= 11X There is a 15.19% of reference with a coverageData >= 12X There is a 11.68% of reference with a coverageData >= 13X There is a 8.88% of reference with a coverageData >= 14X There is a 6.69% of reference with a coverageData >= 15X There is a 5% of reference with a coverageData >= 16X There is a 3.72% of reference with a coverageData >= 17X There is a 2.75% of reference with a coverageData >= 18X There is a 2.03% of reference with a coverageData >= 19X There is a 1.51% of reference with a coverageData >= 20X There is a 1.12% of reference with a coverageData >= 21X There is a 0.85% of reference with a coverageData >= 22X There is a 0.65% of reference with a coverageData >= 23X There is a 0.5% of reference with a coverageData >= 24X There is a 0.4% of reference with a coverageData >= 25X There is a 0.32% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1837500675 7.3721006897712 236.13913376106026 chr2 243199373 2275828572 9.357871872473947 50.82327825973977 chr3 198022430 1423320425 7.1876727550510315 14.085263716641826 chr4 191154276 1206407987 6.311174472497806 77.21277677221298 chr5 180915260 1170084087 6.467580938169616 8.26981924191715 chr6 171115067 1326134735 7.749958891697129 27.653384774121925 chr7 159138663 1123669036 7.060943046882328 59.65333648919229 chr8 146364022 1237695473 8.456282193447786 96.59820507221066 chr9 141213431 1097347461 7.770843419277873 77.56220767490068 chr10 135534747 962344223 7.100350606033152 222.44100104732348 chr11 135006516 960587874 7.115122310096499 36.89072580815928 chr12 133851895 1094651932 8.178083186644463 7.9451605181074605 chr13 115169878 608784284 5.285967950751845 4.727097233941928 chr14 107349540 430636482 4.0115354197139546 6.831081172583345 chr15 102531392 530094648 5.1700716986267 4.642734970290541 chr16 90354753 587990630 6.507578300833826 85.87856090784692 chr17 81195210 463560914 5.709215038670385 24.660758807913833 chr18 78077248 683179428 8.750044929862282 80.94610622725907 chr19 59128983 378786720 6.406109166464101 103.60535213257319 chr20 63025520 420345895 6.6694554047312895 22.68088209346382 chr21 48129895 271122634 5.633144098901525 31.206890554771796 chr22 51304566 250160774 4.8759943510680905 6.302344726504713 chrMT 16571 8641152 521.4623136805262 109.6017290829122 chrX 155270560 1258614881 8.105946684290956 25.96936729735086 chrY 59373566 60623103 1.0210453419624483 67.03301871312378