BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926917.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 = 30,092,888 number of mapped reads = 28,200,032 (93.71%) number of supplementary alignments = 248,077 (0.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,207,887 number of mapped paired reads (second in pair) = 13,992,145 number of mapped paired reads (both in pair) = 27,815,496 number of mapped paired reads (singletons) = 384,536 number of mapped bases = 2,638,641,794 bp number of sequenced bases = 2,636,595,750 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,104,555 duplication rate = 5.85% >>>>>>> Insert size mean insert size = 109,392.5182 std insert size = 3,286,096.3952 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.3753 >>>>>>> ACTG content number of A's = 750,784,021 bp (28.48%) number of C's = 527,627,182 bp (20.01%) number of T's = 756,874,924 bp (28.71%) number of G's = 601,060,562 bp (22.8%) number of N's = 249,061 bp (0.01%) GC percentage = 42.81% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 27,257,099 number of insertions = 421,230 mapped reads with insertion percentage = 1.47% number of deletions = 1,450,733 mapped reads with deletion percentage = 5.01% homopolymer indels = 53.04% >>>>>>> Coverage mean coverageData = 0.8524X std coverageData = 3.5564X There is a 32.6% of reference with a coverageData >= 1X There is a 18.47% of reference with a coverageData >= 2X There is a 11% of reference with a coverageData >= 3X There is a 6.98% of reference with a coverageData >= 4X There is a 4.57% of reference with a coverageData >= 5X There is a 3.08% of reference with a coverageData >= 6X There is a 2.11% of reference with a coverageData >= 7X There is a 1.47% of reference with a coverageData >= 8X There is a 1.03% of reference with a coverageData >= 9X There is a 0.74% of reference with a coverageData >= 10X There is a 0.53% of reference with a coverageData >= 11X There is a 0.39% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 217499058 0.8726119001324374 3.1280927562220575 chr2 243199373 226736710 0.9323079545932875 4.666421013446989 chr3 198022430 177277997 0.8952420036457486 1.9180802604640474 chr4 191154276 153288783 0.8019113472512642 1.922264729584679 chr5 180915260 159656922 0.8824956059538592 1.8227396269020182 chr6 171115067 150167451 0.8775816977005304 1.8278304049902638 chr7 159138663 135210833 0.8496416298281958 2.121230796998949 chr8 146364022 134093950 0.9161674308184835 2.1361503850316517 chr9 141213431 115269948 0.816281760054396 3.622067627066877 chr10 135534747 133265270 0.9832553861630774 11.555843729950864 chr11 135006516 126515086 0.9371035543202967 2.384711491767947 chr12 133851895 118994772 0.889003267379965 1.91089840542642 chr13 115169878 78262455 0.679539271544596 1.6107774996105335 chr14 107349540 78665292 0.7327957995907575 1.7584894182827469 chr15 102531392 79902600 0.7792988902364654 1.8577734976852767 chr16 90354753 84828168 0.9388345956742309 4.675028253689784 chr17 81195210 70339897 0.8663059926810953 2.0992135420620337 chr18 78077248 69371201 0.8884944433492328 3.596245074231729 chr19 59128983 43702660 0.7391072496545391 2.153806119183154 chr20 63025520 64222987 1.018999716305395 2.171416946105604 chr21 48129895 34035395 0.7071570590378392 2.5472444149703866 chr22 51304566 35115901 0.6844595664253353 1.7852565960969375 chrMT 16571 174793 10.548126244644259 7.372367702911347 chrX 155270560 148279553 0.9549753217866929 2.0424430040475556 chrY 59373566 3764112 0.06339710166642172 1.5266658075714343