BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006183.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 4,594,652 number of mapped reads = 4,052,686 (88.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,032,887 number of mapped paired reads (second in pair) = 2,019,799 number of mapped paired reads (both in pair) = 3,738,038 number of mapped paired reads (singletons) = 314,648 number of mapped bases = 156,904,724 bp number of sequenced bases = 156,883,482 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 135,557 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 82,665.1871 std insert size = 2,752,719.5301 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 47.7789 >>>>>>> ACTG content number of A's = 43,847,474 bp (27.95%) number of C's = 33,812,266 bp (21.55%) number of T's = 44,739,765 bp (28.52%) number of G's = 34,478,037 bp (21.98%) number of N's = 5,940 bp (0%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 462,709 number of insertions = 4,348 mapped reads with insertion percentage = 0.11% number of deletions = 15,707 mapped reads with deletion percentage = 0.39% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.3515X There is a 4.45% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.06% 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% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% 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 14356118 0.057597120289622064 0.5204602525983905 chr2 243199373 8374535 0.03443485440235901 0.2546511344209356 chr3 198022430 11250627 0.056814912330891 0.2614051554028588 chr4 191154276 10559840 0.05524249951907955 0.28531212302984854 chr5 180915260 10427067 0.05763508838336799 0.26326887577464103 chr6 171115067 9574083 0.05595113959193319 0.28299650045738123 chr7 159138663 8997024 0.056535752094385765 0.37839912432829803 chr8 146364022 6877317 0.04698775632170042 0.7726131865688513 chr9 141213431 6094063 0.04315498148331231 0.255556436842257 chr10 135534747 8286618 0.061140173892086876 0.3942647248757799 chr11 135006516 7943487 0.058837804539745325 0.3012901411869177 chr12 133851895 7907960 0.05907992561479985 0.26748758546519963 chr13 115169878 3317659 0.028806655504141455 0.18725878529347406 chr14 107349540 2627507 0.024476183130360877 0.23994895848899678 chr15 102531392 4914197 0.04792870655652466 0.24049742804848448 chr16 90354753 5251818 0.05812442429010901 0.3395249191975992 chr17 81195210 4760060 0.058624886862168345 0.2760892159124732 chr18 78077248 4362675 0.05587639308188731 0.41617211344666677 chr19 59128983 3632932 0.061440799683633994 0.39037656590534164 chr20 63025520 3687308 0.05850499924475038 0.27438753569267066 chr21 48129895 2260812 0.04697313384955442 0.26386364509543536 chr22 51304566 2257247 0.04399700018902801 0.23606628610150449 chrMT 16571 20195 1.2186953110856316 1.3083395392813018 chrX 155270560 8718761 0.056152054838985575 0.27508248039845173 chrY 59373566 444814 0.007491785148966798 0.2272114809224728