BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080747.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 5,309,022 number of mapped reads = 4,344,962 (81.84%) number of supplementary alignments = 29,901 (0.56%) number of secondary alignments = 0 number of mapped bases = 277,287,133 bp number of sequenced bases = 277,205,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 601,512 duplication rate = 10.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4527 >>>>>>> ACTG content number of A's = 81,657,150 bp (29.46%) number of C's = 56,733,963 bp (20.47%) number of T's = 77,803,696 bp (28.07%) number of G's = 60,384,108 bp (21.78%) number of N's = 626,834 bp (0.23%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 2,767,541 number of insertions = 18,280 mapped reads with insertion percentage = 0.42% number of deletions = 45,001 mapped reads with deletion percentage = 1.03% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.0896X std coverageData = 0.5342X There is a 5.63% of reference with a coverageData >= 1X There is a 1.85% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 32795286 0.13157554379774244 0.7943129602737643 chr2 243199373 20922173 0.08602889366824149 0.4919166151670778 chr3 198022430 17878273 0.09028408044482637 0.449010250597132 chr4 191154276 15405073 0.08058973789317692 0.4567049731850313 chr5 180915260 20113936 0.11117876955210965 0.49833307908426916 chr6 171115067 18991347 0.11098582569587516 0.5737970255120035 chr7 159138663 18900053 0.11876468385309986 0.6896480613657021 chr8 146364022 11961075 0.0817214151166193 0.6104734602551593 chr9 141213431 10902606 0.07720657959227689 0.47125506673744033 chr10 135534747 13546630 0.09994949855921449 0.538625403513252 chr11 135006516 10155886 0.07522515431773678 0.4784523558039769 chr12 133851895 10587916 0.07910172657622815 0.4270304629121169 chr13 115169878 12432021 0.10794507397151189 0.5023506712340223 chr14 107349540 8072561 0.07519884109424223 0.45254087549119726 chr15 102531392 6761867 0.06594923630803724 0.3883831778004333 chr16 90354753 5560933 0.06154555034863523 0.39647083211564604 chr17 81195210 7388446 0.09099608215804848 0.47325587441853656 chr18 78077248 3696076 0.04733870742985204 0.6407485541080014 chr19 59128983 4414511 0.0746590043667756 0.6477205805658954 chr20 63025520 4877826 0.07739445862564878 0.4315454114387608 chr21 48129895 5060297 0.10513833450083362 0.5784247315405022 chr22 51304566 1942922 0.03787035251404329 0.29634803563230877 chrMT 16571 6591 0.397743045078752 0.977486943091227 chrX 155270560 14202245 0.09146772575561007 0.47455928742604536 chrY 59373566 710583 0.01196800273037331 0.2981546247184314