BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038497.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 12,526,106 number of mapped reads = 12,211,315 (97.49%) number of supplementary alignments = 185,663 (1.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,178,630 number of mapped paired reads (second in pair) = 6,032,685 number of mapped paired reads (both in pair) = 12,051,740 number of mapped paired reads (singletons) = 159,575 number of mapped bases = 1,755,644,348 bp number of sequenced bases = 1,754,456,965 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,523,941 duplication rate = 8.22% >>>>>>> Insert size mean insert size = 84,765.6012 std insert size = 2,764,674.5332 median insert size = 263 >>>>>>> Mapping quality mean mapping quality = 53.8858 >>>>>>> ACTG content number of A's = 509,692,283 bp (29.05%) number of C's = 360,814,466 bp (20.57%) number of T's = 510,191,885 bp (29.08%) number of G's = 373,721,600 bp (21.3%) number of N's = 36,731 bp (0%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.014 number of mismatches = 23,778,262 number of insertions = 290,704 mapped reads with insertion percentage = 2.24% number of deletions = 597,004 mapped reads with deletion percentage = 4.7% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.5671X std coverageData = 6.5607X There is a 23.76% of reference with a coverageData >= 1X There is a 12.58% of reference with a coverageData >= 2X There is a 6.66% of reference with a coverageData >= 3X There is a 3.92% of reference with a coverageData >= 4X There is a 2.32% of reference with a coverageData >= 5X There is a 1.44% of reference with a coverageData >= 6X There is a 0.91% of reference with a coverageData >= 7X There is a 0.6% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 104715822 0.4201226122521877 4.076587145001039 chr2 243199373 192209361 0.7903365811720247 7.415216207682339 chr3 198022430 110258108 0.5567960558811443 1.347391414712096 chr4 191154276 98878916 0.5172728440560754 5.572612373170442 chr5 180915260 100151516 0.5535824672833016 1.4150013950643856 chr6 171115067 120326061 0.7031879957128497 8.255571051703066 chr7 159138663 115175182 0.7237410433692031 5.960741915158586 chr8 146364022 76659900 0.5237619119266892 1.8127539958727932 chr9 141213431 68787286 0.48711574750988096 8.745407793612632 chr10 135534747 72652162 0.5360408574784148 18.235264418921414 chr11 135006516 98775138 0.7316323754329014 3.7638021365100243 chr12 133851895 59521900 0.4446847764090303 1.2061225469224164 chr13 115169878 114272779 0.9922106455648064 2.068229007217165 chr14 107349540 32217733 0.3001198980452082 1.0222499357942396 chr15 102531392 30544248 0.29790142710634415 0.9192075875261145 chr16 90354753 69275400 0.7667045473523678 14.249033985653272 chr17 81195210 37089352 0.4567923649683276 3.5697978343004633 chr18 78077248 26616324 0.3408973123642883 7.876857786913746 chr19 59128983 19409518 0.3282572609104405 2.353494727377983 chr20 63025520 55784443 0.8851088098916121 2.4439122905756636 chr21 48129895 14882269 0.3092105021213946 2.7579695967726905 chr22 51304566 10064926 0.19617992675349794 0.8378350591764342 chrMT 16571 656283 39.604308732122384 18.924170567536837 chrX 155270560 104008546 0.6698536155211908 1.7336492557639873 chrY 59373566 22711175 0.3825132382986732 10.608758508023838