BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046543.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 10,134,932 number of mapped reads = 9,984,225 (98.51%) number of supplementary alignments = 53,882 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,051,050 number of mapped paired reads (second in pair) = 4,933,175 number of mapped paired reads (both in pair) = 9,851,126 number of mapped paired reads (singletons) = 133,099 number of mapped bases = 953,749,508 bp number of sequenced bases = 953,500,606 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,411,870 duplication rate = 34.43% >>>>>>> Insert size mean insert size = 31,857.3414 std insert size = 1,874,211.469 median insert size = 122 >>>>>>> Mapping quality mean mapping quality = 52.4807 >>>>>>> ACTG content number of A's = 283,976,653 bp (29.78%) number of C's = 193,588,819 bp (20.3%) number of T's = 281,873,256 bp (29.56%) number of G's = 193,979,972 bp (20.34%) number of N's = 81,906 bp (0.01%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 3,686,063 number of insertions = 81,735 mapped reads with insertion percentage = 0.81% number of deletions = 90,133 mapped reads with deletion percentage = 0.88% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.3081X std coverageData = 35.5863X There is a 3.37% of reference with a coverageData >= 1X There is a 2.18% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 294070693 1.1798192992265404 100.00848474018456 chr2 243199373 103029946 0.4236439622728797 31.612953344406307 chr3 198022430 23550228 0.1189270730593499 9.658616463650652 chr4 191154276 19763539 0.10339051479026291 6.454372834792025 chr5 180915260 37123837 0.20520014176802995 13.54275414952341 chr6 171115067 45423539 0.2654561038742427 18.80532668678355 chr7 159138663 39819455 0.2502186096662129 19.563792171546087 chr8 146364022 65933380 0.45047532241222504 24.31268796483485 chr9 141213431 17769018 0.12583093459431632 18.85799169421053 chr10 135534747 38877477 0.2868450922035513 30.506009713352423 chr11 135006516 68834286 0.5098589908060438 56.95892356969348 chr12 133851895 15736070 0.11756329635826224 8.003940884289785 chr13 115169878 36065009 0.31314619435474267 22.939605529633546 chr14 107349540 27807547 0.25903741180446604 20.771969836980624 chr15 102531392 16571409 0.16162278378118577 11.132911539917382 chr16 90354753 20193759 0.2234941530967386 17.785292163478246 chr17 81195210 14921177 0.18376917800939244 10.20817226664202 chr18 78077248 3544237 0.04539397956239441 0.547080447550517 chr19 59128983 1885945 0.03189544119167414 0.5924823998022356 chr20 63025520 13514012 0.21442126935247818 17.243143217545644 chr21 48129895 15564782 0.3233911480588104 37.367062592642824 chr22 51304566 1516630 0.029561306492681374 1.584319501516159 chrMT 16571 99078 5.978999456882506 3.6220957752383782 chrX 155270560 31917277 0.20555910276874123 18.093038610710714 chrY 59373566 217178 0.0036578230790449743 0.18873843799332865