BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927052.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 30,420,902 number of mapped reads = 29,867,334 (98.18%) number of supplementary alignments = 531,667 (1.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,977,018 number of mapped paired reads (second in pair) = 14,890,316 number of mapped paired reads (both in pair) = 29,558,156 number of mapped paired reads (singletons) = 309,178 number of mapped bases = 2,848,759,897 bp number of sequenced bases = 2,846,587,186 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,150,040 duplication rate = 5.75% >>>>>>> Insert size mean insert size = 167,999.7998 std insert size = 3,989,551.9529 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 53.3841 >>>>>>> ACTG content number of A's = 813,362,863 bp (28.57%) number of C's = 578,330,449 bp (20.32%) number of T's = 820,978,429 bp (28.84%) number of G's = 633,660,027 bp (22.26%) number of N's = 255,418 bp (0.01%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 26,769,597 number of insertions = 470,735 mapped reads with insertion percentage = 1.55% number of deletions = 1,521,612 mapped reads with deletion percentage = 4.96% homopolymer indels = 52.74% >>>>>>> Coverage mean coverageData = 0.9202X std coverageData = 3.4247X There is a 33.7% of reference with a coverageData >= 1X There is a 19.82% of reference with a coverageData >= 2X There is a 12.03% of reference with a coverageData >= 3X There is a 7.75% of reference with a coverageData >= 4X There is a 5.13% of reference with a coverageData >= 5X There is a 3.48% of reference with a coverageData >= 6X There is a 2.41% of reference with a coverageData >= 7X There is a 1.7% of reference with a coverageData >= 8X There is a 1.21% of reference with a coverageData >= 9X There is a 0.87% of reference with a coverageData >= 10X There is a 0.64% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% 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 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 236847363 0.9502378050243654 4.773534804646206 chr2 243199373 251389068 1.0336748195481573 5.503960510557589 chr3 198022430 190230883 0.9606532098409256 1.9714024515120971 chr4 191154276 165245990 0.8644639997485591 2.974735539980564 chr5 180915260 172387830 0.9528650595864605 1.9494931078686895 chr6 171115067 167105333 0.9765670313532355 2.014368151356745 chr7 159138663 148190522 0.9312037641035101 2.6974142509714243 chr8 146364022 142088292 0.970787014858064 2.38361198913697 chr9 141213431 125854559 0.8912364646107919 4.5192068205493365 chr10 135534747 139677154 1.0305634318260837 5.063536716331302 chr11 135006516 140813396 1.0430118498873047 3.8743968335119074 chr12 133851895 126471563 0.9448619535793648 2.306344027794022 chr13 115169878 84956830 0.7376653642022613 1.76474282360066 chr14 107349540 83884679 0.7814162873916367 1.8392587406846042 chr15 102531392 87000328 0.8485238160035904 1.9616426038359576 chr16 90354753 89010658 0.9851242468672345 4.363208374923008 chr17 81195210 69160844 0.8517847789296931 2.5127869021341587 chr18 78077248 76035187 0.9738456329813264 4.675239467971395 chr19 59128983 46116011 0.7799222760181754 2.949069166911632 chr20 63025520 68070437 1.080045622788991 2.3223583801833176 chr21 48129895 36530671 0.7590016766086857 2.819580915862825 chr22 51304566 37899958 0.7387248534565131 1.9109215705759566 chrMT 16571 154932 9.34958662724036 7.9394656694119075 chrX 155270560 158280202 1.0193832108288912 2.3462313058580384 chrY 59373566 5357207 0.09022882337907748 3.9577452935693342