BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093999.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 408,108 number of mapped reads = 385,027 (94.34%) number of supplementary alignments = 21,032 (5.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 193,450 number of mapped paired reads (second in pair) = 191,577 number of mapped paired reads (both in pair) = 381,624 number of mapped paired reads (singletons) = 3,403 number of mapped bases = 49,882,713 bp number of sequenced bases = 48,923,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 363,650 duplication rate = 50.84% >>>>>>> Insert size mean insert size = 903,067.4671 std insert size = 8,608,052.8366 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 40.3845 >>>>>>> ACTG content number of A's = 12,989,867 bp (26.55%) number of C's = 11,423,941 bp (23.35%) number of T's = 12,337,926 bp (25.22%) number of G's = 12,170,990 bp (24.88%) number of N's = 555 bp (0%) GC percentage = 48.23% >>>>>>> Mismatches and indels general error rate = 0.0366 number of mismatches = 1,722,253 number of insertions = 29,323 mapped reads with insertion percentage = 7.51% number of deletions = 138,328 mapped reads with deletion percentage = 34.52% homopolymer indels = 28.52% >>>>>>> Coverage mean coverageData = 0.0161X std coverageData = 2.9698X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 710799 0.0028517441487136757 0.9444295674468399 chr2 243199373 2525062 0.010382683017854655 3.1013334840281654 chr3 198022430 876128 0.004424387681738882 1.5255559835200974 chr4 191154276 1304246 0.006823001960991969 2.29519188666606 chr5 180915260 517073 0.0028580949998358346 1.3968834500934582 chr6 171115067 1058295 0.006184697926103725 1.7128986696109099 chr7 159138663 1174622 0.007381122713089527 2.0194398392683035 chr8 146364022 568087 0.0038813295250932638 1.3208368144305258 chr9 141213431 778033 0.005509624647530871 1.66111487433816 chr10 135534747 971576 0.00716846433483216 2.1082154412804623 chr11 135006516 1220115 0.00903745268117281 2.2173087842982433 chr12 133851895 1315801 0.009830275469764548 2.3368449439452497 chr13 115169878 1090793 0.009471165715743834 2.5359002485423776 chr14 107349540 172120 0.001603360387012371 0.5382493416731373 chr15 102531392 713190 0.006955820906049925 1.6682140086601334 chr16 90354753 268743 0.002974309497586696 0.7890082835415028 chr17 81195210 1042534 0.01283984609436936 3.0695735931505865 chr18 78077248 248472 0.0031823867562545236 0.925257934969027 chr19 59128983 92223 0.0015596919703489572 0.41566643013475685 chr20 63025520 347501 0.005513655420851744 1.777101299926733 chr21 48129895 96949 0.0020143197902260123 0.35314797544009763 chr22 51304566 144030 0.0028073524683943337 0.7875598853697429 chrMT 16571 1105853 66.73423450606481 280.6154573615481 chrX 155270560 30700586 0.19772316142867005 9.914542143337194 chrY 59373566 839882 0.014145722694169995 2.2074817559887343