BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777259.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 33,888,478 number of mapped reads = 33,766,578 (99.64%) number of supplementary alignments = 858,623 (2.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,883,520 number of mapped paired reads (second in pair) = 16,883,058 number of mapped paired reads (both in pair) = 33,742,728 number of mapped paired reads (singletons) = 23,850 number of mapped bases = 3,393,269,093 bp number of sequenced bases = 3,392,761,180 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,576,898 duplication rate = 35.17% >>>>>>> Insert size mean insert size = 157,100.391 std insert size = 3,915,134.329 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 54.7817 >>>>>>> ACTG content number of A's = 930,594,523 bp (27.43%) number of C's = 766,690,943 bp (22.6%) number of T's = 927,167,123 bp (27.33%) number of G's = 768,179,966 bp (22.64%) number of N's = 128,625 bp (0%) GC percentage = 45.24% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 8,652,938 number of insertions = 615,625 mapped reads with insertion percentage = 1.8% number of deletions = 224,076 mapped reads with deletion percentage = 0.65% homopolymer indels = 51.77% >>>>>>> Coverage mean coverageData = 1.0961X std coverageData = 12.5635X There is a 12.43% of reference with a coverageData >= 1X There is a 6.31% of reference with a coverageData >= 2X There is a 3.97% of reference with a coverageData >= 3X There is a 3.06% of reference with a coverageData >= 4X There is a 2.54% of reference with a coverageData >= 5X There is a 2.23% of reference with a coverageData >= 6X There is a 2.02% of reference with a coverageData >= 7X There is a 1.86% of reference with a coverageData >= 8X There is a 1.73% of reference with a coverageData >= 9X There is a 1.62% of reference with a coverageData >= 10X There is a 1.53% of reference with a coverageData >= 11X There is a 1.46% of reference with a coverageData >= 12X There is a 1.39% of reference with a coverageData >= 13X There is a 1.32% of reference with a coverageData >= 14X There is a 1.27% of reference with a coverageData >= 15X There is a 1.22% of reference with a coverageData >= 16X There is a 1.17% of reference with a coverageData >= 17X There is a 1.13% of reference with a coverageData >= 18X There is a 1.09% of reference with a coverageData >= 19X There is a 1.05% of reference with a coverageData >= 20X There is a 1.01% of reference with a coverageData >= 21X There is a 0.98% of reference with a coverageData >= 22X There is a 0.95% of reference with a coverageData >= 23X There is a 0.92% of reference with a coverageData >= 24X There is a 0.89% of reference with a coverageData >= 25X There is a 0.87% of reference with a coverageData >= 26X There is a 0.84% of reference with a coverageData >= 27X There is a 0.82% of reference with a coverageData >= 28X There is a 0.8% of reference with a coverageData >= 29X There is a 0.77% of reference with a coverageData >= 30X There is a 0.75% of reference with a coverageData >= 31X There is a 0.74% of reference with a coverageData >= 32X There is a 0.72% of reference with a coverageData >= 33X There is a 0.7% of reference with a coverageData >= 34X There is a 0.68% of reference with a coverageData >= 35X There is a 0.66% of reference with a coverageData >= 36X There is a 0.65% of reference with a coverageData >= 37X There is a 0.63% of reference with a coverageData >= 38X There is a 0.62% of reference with a coverageData >= 39X There is a 0.6% of reference with a coverageData >= 40X There is a 0.59% of reference with a coverageData >= 41X There is a 0.58% of reference with a coverageData >= 42X There is a 0.57% of reference with a coverageData >= 43X There is a 0.55% of reference with a coverageData >= 44X There is a 0.54% of reference with a coverageData >= 45X There is a 0.53% of reference with a coverageData >= 46X There is a 0.52% of reference with a coverageData >= 47X There is a 0.51% of reference with a coverageData >= 48X There is a 0.5% of reference with a coverageData >= 49X There is a 0.49% of reference with a coverageData >= 50X There is a 0.48% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 343315934 1.3773924920331493 13.91187084882871 chr2 243199373 313025668 1.2871154400550202 13.315650649114804 chr3 198022430 200064470 1.0103121651421003 11.760668137019614 chr4 191154276 148736106 0.7780945794798751 9.831673800320493 chr5 180915260 169799392 0.9385575987343466 10.799991426353454 chr6 171115067 161688727 0.944912273563847 11.475298081423565 chr7 159138663 217420265 1.3662315674978367 15.875234669501475 chr8 146364022 111600525 0.7624860500212272 10.693499199124915 chr9 141213431 106338354 0.7530328613005657 8.85239273332511 chr10 135534747 147438940 1.0878312998215875 11.964335540167381 chr11 135006516 224774363 1.6649149215879329 16.677236367612654 chr12 133851895 188113969 1.4053889113785054 13.333332175208795 chr13 115169878 98805642 0.8579121877684024 10.679895336136942 chr14 107349540 73425530 0.6839855112560334 8.924093533390305 chr15 102531392 160263812 1.5630706740039186 15.956090239562174 chr16 90354753 106108219 1.174351270707364 13.075622753399655 chr17 81195210 140064502 1.7250340506539734 15.29526637569981 chr18 78077248 49841793 0.638365135512973 8.08471596105127 chr19 59128983 183360132 3.1010195456938603 24.811935919641154 chr20 63025520 90749434 1.439883939077377 14.256517346954109 chr21 48129895 22565847 0.46885302783228594 7.141809430326876 chr22 51304566 39386898 0.7677074590203141 8.664732085792513 chrMT 16571 862079 52.023354052259975 27.488188432965938 chrX 155270560 94514094 0.6087058229196829 10.007191413257122 chrY 59373566 1004398 0.016916585404353177 0.5871073687288181