BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926956.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 = 14,512,394 number of mapped reads = 14,106,414 (97.2%) number of supplementary alignments = 543,318 (3.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,041,663 number of mapped paired reads (second in pair) = 7,064,751 number of mapped paired reads (both in pair) = 13,870,952 number of mapped paired reads (singletons) = 235,462 number of mapped bases = 1,284,884,043 bp number of sequenced bases = 1,283,914,839 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,062,656 duplication rate = 6.22% >>>>>>> Insert size mean insert size = 459,440.3413 std insert size = 6,809,803.0187 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 51.977 >>>>>>> ACTG content number of A's = 361,418,584 bp (28.15%) number of C's = 257,000,005 bp (20.02%) number of T's = 366,773,036 bp (28.57%) number of G's = 298,671,500 bp (23.26%) number of N's = 51,714 bp (0%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 12,185,980 number of insertions = 221,438 mapped reads with insertion percentage = 1.54% number of deletions = 652,016 mapped reads with deletion percentage = 4.5% homopolymer indels = 51.76% >>>>>>> Coverage mean coverageData = 0.4151X std coverageData = 1.5827X There is a 20.77% of reference with a coverageData >= 1X There is a 9.43% of reference with a coverageData >= 2X There is a 4.52% of reference with a coverageData >= 3X There is a 2.42% of reference with a coverageData >= 4X There is a 1.37% of reference with a coverageData >= 5X There is a 0.82% of reference with a coverageData >= 6X There is a 0.51% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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% 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 129667986 0.5202313457826852 1.818356007558725 chr2 243199373 130876234 0.5381437969414502 2.904770737601364 chr3 198022430 98301501 0.49641599186516394 1.1912545093688953 chr4 191154276 80039839 0.41871853810897747 1.5461477125318202 chr5 180915260 11349994 0.0627365209546171 0.44907132986568543 chr6 171115067 83934899 0.4905172903330599 1.2382094793008591 chr7 159138663 11450057 0.07195018975369927 0.6216032038362888 chr8 146364022 72165518 0.49305503506865916 1.2209948926451817 chr9 141213431 66823427 0.47320872049344936 1.5078704315523468 chr10 135534747 73570850 0.5428191045356067 2.6072038966546045 chr11 135006516 76067458 0.5634354567004751 1.496716950931649 chr12 133851895 68465971 0.5115054291909726 1.3889489678361104 chr13 115169878 42741897 0.3711204504358336 1.004103493092876 chr14 107349540 48704356 0.4536987862267505 1.1645074483760796 chr15 102531392 50518392 0.4927114614809872 1.237985239405863 chr16 90354753 8359027 0.09251341763946828 0.9797190895910629 chr17 81195210 49179333 0.6056925402372874 1.4774153099382854 chr18 78077248 4485084 0.057444186557395055 0.9897163489661218 chr19 59128983 36869624 0.6235457153051321 1.639366198848184 chr20 63025520 39579938 0.6279985948549096 1.5278307850724997 chr21 48129895 18488053 0.3841282637329668 1.531737429572126 chr22 51304566 2857100 0.0556890004683014 0.4452788977763949 chrMT 16571 1146385 69.18019431537023 73.58777457095516 chrX 155270560 76140397 0.4903723989917986 1.1979956355121155 chrY 59373566 3100723 0.05222396444909507 1.1466224869376886