BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617379.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 28,984,323 (90.58%) number of supplementary alignments = 62,760 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,678,052 number of mapped paired reads (second in pair) = 14,306,271 number of mapped paired reads (both in pair) = 28,199,702 number of mapped paired reads (singletons) = 784,621 number of mapped bases = 2,832,263,038 bp number of sequenced bases = 2,831,449,263 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,453,049 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 51,123.6562 std insert size = 2,162,706.2094 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 53.312 >>>>>>> ACTG content number of A's = 860,224,369 bp (30.38%) number of C's = 559,972,241 bp (19.78%) number of T's = 846,749,249 bp (29.91%) number of G's = 563,224,331 bp (19.89%) number of N's = 1,279,073 bp (0.05%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0157 number of mismatches = 43,783,197 number of insertions = 286,317 mapped reads with insertion percentage = 0.96% number of deletions = 341,231 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.74% >>>>>>> Coverage mean coverageData = 0.9149X std coverageData = 9.1073X There is a 51.5% of reference with a coverageData >= 1X There is a 22.7% of reference with a coverageData >= 2X There is a 8.54% of reference with a coverageData >= 3X There is a 2.95% of reference with a coverageData >= 4X There is a 1% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 183544327 0.7363846327187286 18.64112566076682 chr2 243199373 279642996 1.149850809853856 8.07251371880434 chr3 198022430 226344696 1.1430255451364777 1.4439515541453565 chr4 191154276 155880836 0.8154713525738759 8.17689400001707 chr5 180915260 178807310 0.9883484124003691 1.4078158820068545 chr6 171115067 133300660 0.7790118213260554 3.4916337633116132 chr7 159138663 230246475 1.4468292661224633 10.439569507165743 chr8 146364022 119566602 0.8169125196627898 7.076417331149654 chr9 141213431 118837066 0.8415422326223346 13.506067675979269 chr10 135534747 119213316 0.8795775152773185 19.07977147371446 chr11 135006516 151619596 1.1230539124496777 5.073274934118469 chr12 133851895 125019971 0.9340171911649066 1.2920130962865177 chr13 115169878 124306682 1.0793332784462966 1.2645593826038553 chr14 107349540 82134491 0.7651126497607722 1.33775644484591 chr15 102531392 63504361 0.619365052607498 0.95174491369623 chr16 90354753 70878672 0.7844487384078179 7.715685441122865 chr17 81195210 87050708 1.0721162984860806 6.579149575626762 chr18 78077248 51031444 0.6536019814632811 14.004815309267391 chr19 59128983 51760617 0.8753848683648086 9.084732316176979 chr20 63025520 80327588 1.2745247956700714 2.2601796252572184 chr21 48129895 44910337 0.9331068974906345 3.0148464267025195 chr22 51304566 24644116 0.4803493708532687 0.8780037571979173 chrMT 16571 1913720 115.48609015750408 23.37970402333655 chrX 155270560 118409838 0.7626032777881396 2.779847324631179 chrY 59373566 9366613 0.15775729219296009 7.390497358971646