BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124931.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,290,218 number of mapped reads = 4,227,130 (98.53%) number of supplementary alignments = 19,669 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,117,969 number of mapped paired reads (second in pair) = 2,109,161 number of mapped paired reads (both in pair) = 4,207,008 number of mapped paired reads (singletons) = 20,122 number of mapped bases = 367,768,359 bp number of sequenced bases = 367,568,305 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 342,524 duplication rate = 5.05% >>>>>>> Insert size mean insert size = 36,454.7804 std insert size = 1,777,525.5784 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 52.7288 >>>>>>> ACTG content number of A's = 103,966,115 bp (28.28%) number of C's = 68,284,172 bp (18.58%) number of T's = 110,021,661 bp (29.93%) number of G's = 85,284,488 bp (23.2%) number of N's = 11,869 bp (0%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 2,696,410 number of insertions = 52,206 mapped reads with insertion percentage = 1.2% number of deletions = 115,582 mapped reads with deletion percentage = 2.68% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.1188X std coverageData = 1.4087X There is a 8.45% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 29461631 0.1182008328877945 1.2532803112492892 chr2 243199373 33682540 0.13849764324844702 1.4702802297634048 chr3 198022430 31434872 0.15874399682904608 0.5204148743340633 chr4 191154276 23221041 0.12147800973073707 0.7279387853637689 chr5 180915260 16560177 0.09153554542607406 0.45044910094130375 chr6 171115067 23422843 0.136883580216814 3.6339400912161777 chr7 159138663 19668236 0.12359181376307025 1.1507436079200157 chr8 146364022 24148703 0.1649907037946798 0.6510155127930494 chr9 141213431 20784929 0.14718804615688433 1.5793669655540976 chr10 135534747 17459380 0.1288184792937268 2.473450407419752 chr11 135006516 14175097 0.10499565072844336 1.344920074656989 chr12 133851895 16555012 0.12368156610707678 0.5110965556924477 chr13 115169878 8250269 0.07163564938394743 0.328540320881774 chr14 107349540 8031285 0.07481434014528614 0.41635006134319097 chr15 102531392 13433112 0.13101462623271515 0.4772320091582462 chr16 90354753 12441280 0.1376936971981983 2.1881556122415944 chr17 81195210 7151622 0.0880793583759436 0.9774052291011599 chr18 78077248 7488232 0.0959079910193556 1.5068544869152518 chr19 59128983 3805222 0.06435459916501524 0.9060770335022986 chr20 63025520 9928776 0.15753580454393712 0.547038981921943 chr21 48129895 4904380 0.10189883023846198 0.6132351435872897 chr22 51304566 5113784 0.0996750269751819 0.42626624789521134 chrMT 16571 87800 5.298412889988534 3.5319351162269683 chrX 155270560 15087726 0.09717055184189456 0.6444906398519373 chrY 59373566 1470410 0.02476539812346794 1.5205820082888635