BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549017.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,313,285 number of mapped reads = 8,103,695 (87.01%) number of secondary alignments = 0 number of mapped bases = 320,646,211 bp number of sequenced bases = 320,611,941 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 416,822 duplication rate = 4.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.475 >>>>>>> ACTG content number of A's = 93,518,132 bp (29.17%) number of C's = 66,126,127 bp (20.62%) number of T's = 94,484,992 bp (29.47%) number of G's = 66,470,864 bp (20.73%) number of N's = 11,826 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 791,975 number of insertions = 10,628 mapped reads with insertion percentage = 0.13% number of deletions = 26,098 mapped reads with deletion percentage = 0.32% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 0.1036X std coverageData = 1.2665X There is a 7.43% of reference with a coverageData >= 1X There is a 1.95% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 25986113 0.104256963917454 1.0031827819538603 chr2 243199373 25551632 0.10506454718532518 0.5547911743516873 chr3 198022430 21028728 0.10619366705074773 0.42834174939738173 chr4 191154276 21237391 0.11110078960514595 0.45116954023101974 chr5 180915260 20011524 0.11061269237321385 0.4415813803833984 chr6 171115067 19154221 0.11193766472943029 0.48250760818011046 chr7 159138663 19106055 0.12005916500630648 0.9715563931680326 chr8 146364022 17598095 0.12023511488362898 5.1637321155531115 chr9 141213431 13263096 0.09392234085722342 0.5202752874044894 chr10 135534747 14471196 0.10677111456887141 0.521665848285867 chr11 135006516 15067182 0.11160336883295321 0.7317703981777346 chr12 133851895 15862677 0.11850917015407215 0.46372043923429035 chr13 115169878 10386071 0.09018044631426977 0.39162854851152135 chr14 107349540 9692136 0.09028577113604772 0.4311452408524252 chr15 102531392 8523121 0.08312694125912189 0.3760957389799058 chr16 90354753 8811021 0.09751585508733558 0.4269361212396418 chr17 81195210 7935149 0.09772927491658683 0.44851519005283835 chr18 78077248 8484267 0.10866503645210446 0.8412029228227841 chr19 59128983 5976606 0.10107743608578554 0.8691191638707243 chr20 63025520 6478485 0.10279145654014438 0.4330345698062417 chr21 48129895 3810807 0.07917754651241188 0.40091158455544407 chr22 51304566 3517212 0.0685555355833241 0.4656447267089852 chrMT 16571 17236 1.0401303481986603 1.523819948497292 chrX 155270560 17838508 0.1148866082533611 0.5169949855841122 chrY 59373566 837682 0.014108669167689877 0.19986867181702478