BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975268.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 2,121,466 number of mapped reads = 2,093,695 (98.69%) number of supplementary alignments = 24,722 (1.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,048,619 number of mapped paired reads (second in pair) = 1,045,076 number of mapped paired reads (both in pair) = 2,086,688 number of mapped paired reads (singletons) = 7,007 number of mapped bases = 282,632,304 bp number of sequenced bases = 282,419,453 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 314,232 duplication rate = 14.69% >>>>>>> Insert size mean insert size = 66,893.0227 std insert size = 2,456,232.1306 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 53.782 >>>>>>> ACTG content number of A's = 81,862,602 bp (28.99%) number of C's = 58,165,938 bp (20.6%) number of T's = 81,233,291 bp (28.76%) number of G's = 61,139,811 bp (21.65%) number of N's = 17,811 bp (0.01%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 2,909,607 number of insertions = 56,399 mapped reads with insertion percentage = 2.55% number of deletions = 106,468 mapped reads with deletion percentage = 4.89% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.0913X std coverageData = 1.0334X There is a 5.15% of reference with a coverageData >= 1X There is a 2.87% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.05% 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% 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 25665299 0.1029698497722098 0.9897761418639228 chr2 243199373 23727508 0.09756401797960228 1.217869110654487 chr3 198022430 18283902 0.09233247970949554 0.44441179857457896 chr4 191154276 17606663 0.092107084227611 0.7873162303143394 chr5 180915260 15555871 0.08598429452551432 0.4109348219378675 chr6 171115067 22741055 0.13289919700642142 0.8299982771518011 chr7 159138663 15355105 0.09648884005013916 0.915205564324958 chr8 146364022 13951339 0.0953194563073704 0.5091497564876171 chr9 141213431 12187133 0.08630293105759891 1.5698330865093708 chr10 135534747 15556931 0.11478186475679185 2.7985072936650455 chr11 135006516 10294191 0.07624958635329868 0.9360186120264016 chr12 133851895 12296055 0.09186313723836334 0.4226272294653343 chr13 115169878 8781070 0.07624450205634498 0.38737579311888093 chr14 107349540 8350478 0.07778773900661334 0.4045777755127345 chr15 102531392 8301479 0.08096524233280672 0.39678424527708217 chr16 90354753 9945655 0.11007340145127728 1.4649662962490797 chr17 81195210 6520480 0.08030621510800945 0.7641417368410511 chr18 78077248 7778916 0.09963102183109733 1.4184800559720423 chr19 59128983 4604116 0.07786563824376956 0.6496003993075832 chr20 63025520 6166469 0.09784082701737327 0.49832307050460717 chr21 48129895 3461749 0.07192513093992829 0.5551582614226451 chr22 51304566 3461882 0.06747707406783249 0.37117743124793257 chrMT 16571 53066 3.2023414398648242 3.0588749596805953 chrX 155270560 8160189 0.05255464397114302 0.41030335704588333 chrY 59373566 3825703 0.06443444882525667 1.4962376355050004