BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124899.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,586,056 number of mapped reads = 4,545,113 (99.11%) number of supplementary alignments = 22,067 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,274,866 number of mapped paired reads (second in pair) = 2,270,247 number of mapped paired reads (both in pair) = 4,530,686 number of mapped paired reads (singletons) = 14,427 number of mapped bases = 406,652,647 bp number of sequenced bases = 406,439,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 309,428 duplication rate = 4.76% >>>>>>> Insert size mean insert size = 44,010.0033 std insert size = 1,958,684.8186 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.185 >>>>>>> ACTG content number of A's = 115,793,407 bp (28.49%) number of C's = 77,254,671 bp (19.01%) number of T's = 120,847,246 bp (29.73%) number of G's = 92,538,089 bp (22.77%) number of N's = 6,060 bp (0%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 2,915,840 number of insertions = 50,749 mapped reads with insertion percentage = 1.09% number of deletions = 129,161 mapped reads with deletion percentage = 2.79% homopolymer indels = 47.79% >>>>>>> Coverage mean coverageData = 0.1314X std coverageData = 1.128X There is a 8.94% of reference with a coverageData >= 1X There is a 2.5% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 33935867 0.13615158455312334 1.3924417891634264 chr2 243199373 36477364 0.14998954787601365 1.1627511926743666 chr3 198022430 29524282 0.14909564537714237 0.5199725026024536 chr4 191154276 19094019 0.09988800355164433 0.882816800858942 chr5 180915260 23134647 0.12787559766931766 0.47590601994006143 chr6 171115067 20872018 0.12197650601977673 0.7522607546551959 chr7 159138663 28208360 0.1772564848053298 1.6389781435434034 chr8 146364022 36414961 0.24879721465976112 0.8966267086417286 chr9 141213431 20364679 0.14421205444686067 1.4851865378957345 chr10 135534747 21623828 0.15954453362428161 2.696161731738346 chr11 135006516 14997278 0.11108558641717708 0.739622962172379 chr12 133851895 23367447 0.1745768858931732 0.5617660545059399 chr13 115169878 9313750 0.08086966975861518 0.36377117075318377 chr14 107349540 9298860 0.08662226219134242 0.41818016234532795 chr15 102531392 8949938 0.08728973464048942 0.3843855487337142 chr16 90354753 13240512 0.14653918648861783 1.2868326293669472 chr17 81195210 9132452 0.11247525562160625 1.6102125379941417 chr18 78077248 7078466 0.09065977837743461 1.4606872393615307 chr19 59128983 5247750 0.08875089226547327 1.0706713825278502 chr20 63025520 7012119 0.11125840770532318 0.4925111234093826 chr21 48129895 3922189 0.08149174229447208 0.4807063990517167 chr22 51304566 3403341 0.06633602553035922 0.3500655519055673 chrMT 16571 165198 9.969102649206445 6.992594088508622 chrX 155270560 17258968 0.11115415568798104 0.6283792608614828 chrY 59373566 4614354 0.077717312785289 1.1882223248836081