BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960922.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 225,220,794 number of mapped reads = 219,961,387 (97.66%) number of supplementary alignments = 445,200 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 110,578,419 number of mapped paired reads (second in pair) = 109,382,968 number of mapped paired reads (both in pair) = 217,738,228 number of mapped paired reads (singletons) = 2,223,159 number of mapped bases = 21,372,989,472 bp number of sequenced bases = 21,366,820,219 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,624,113 duplication rate = 11.89% >>>>>>> Insert size mean insert size = 18,755.3355 std insert size = 1,268,897.7202 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.5436 >>>>>>> ACTG content number of A's = 6,545,335,085 bp (30.63%) number of C's = 4,149,460,348 bp (19.42%) number of T's = 6,546,975,883 bp (30.64%) number of G's = 4,123,452,924 bp (19.3%) number of N's = 1,595,979 bp (0.01%) GC percentage = 38.72% >>>>>>> Mismatches and indels general error rate = 0.0154 number of mismatches = 323,317,007 number of insertions = 2,623,198 mapped reads with insertion percentage = 1.16% number of deletions = 2,876,454 mapped reads with deletion percentage = 1.27% homopolymer indels = 39.89% >>>>>>> Coverage mean coverageData = 6.9041X std coverageData = 101.7521X There is a 89.34% of reference with a coverageData >= 1X There is a 84.92% of reference with a coverageData >= 2X There is a 78.5% of reference with a coverageData >= 3X There is a 70.59% of reference with a coverageData >= 4X There is a 61.84% of reference with a coverageData >= 5X There is a 52.88% of reference with a coverageData >= 6X There is a 44.24% of reference with a coverageData >= 7X There is a 36.29% of reference with a coverageData >= 8X There is a 29.26% of reference with a coverageData >= 9X There is a 23.24% of reference with a coverageData >= 10X There is a 18.22% of reference with a coverageData >= 11X There is a 14.13% of reference with a coverageData >= 12X There is a 10.87% of reference with a coverageData >= 13X There is a 8.31% of reference with a coverageData >= 14X There is a 6.33% of reference with a coverageData >= 15X There is a 4.81% of reference with a coverageData >= 16X There is a 3.65% of reference with a coverageData >= 17X There is a 2.78% of reference with a coverageData >= 18X There is a 2.13% of reference with a coverageData >= 19X There is a 1.64% of reference with a coverageData >= 20X There is a 1.28% of reference with a coverageData >= 21X There is a 1.01% of reference with a coverageData >= 22X There is a 0.81% of reference with a coverageData >= 23X There is a 0.66% of reference with a coverageData >= 24X There is a 0.55% of reference with a coverageData >= 25X There is a 0.47% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.36% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1774178570 7.118050751014979 269.7841178264584 chr2 243199373 1801458458 7.40733183551423 53.84386822423888 chr3 198022430 1592032523 8.03965754283492 9.310901490499186 chr4 191154276 1414419849 7.399362852861319 54.00997402836549 chr5 180915260 1163923786 6.433530184242059 9.194449146986042 chr6 171115067 1125669256 6.578434475322971 26.739615709870808 chr7 159138663 1177617590 7.399946485663261 67.20648665113954 chr8 146364022 1254456768 8.570800056314386 132.3059356674826 chr9 141213431 912054120 6.458692445479921 95.2600607234415 chr10 135534747 1015775918 7.49457936421278 194.45092809930202 chr11 135006516 1040982226 7.710607286540155 42.122061608490135 chr12 133851895 967037932 7.224686150315615 11.449025930234134 chr13 115169878 739778126 6.423364675266913 4.823583752320272 chr14 107349540 455182581 4.240191257456716 7.284682310789251 chr15 102531392 574302337 5.601234176163335 5.1101942429841865 chr16 90354753 698532011 7.730993531685046 83.97340925870331 chr17 81195210 404522663 4.9821000894018255 25.510205313123546 chr18 78077248 822008549 10.528144498638067 98.22193922012993 chr19 59128983 391443004 6.620154518808484 113.59696846242349 chr20 63025520 399016615 6.331032492869555 18.09919502382191 chr21 48129895 285484460 5.931541300890019 21.699391155449565 chr22 51304566 217687562 4.243044605425568 5.5937945395366855 chrMT 16571 4771731 287.95673163961135 60.518744143149426 chrX 155270560 1082693757 6.972949392338123 28.610675782243636 chrY 59373566 57959080 0.9761765025196566 50.54049344883453