BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695915.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 366,910,526 number of mapped reads = 360,388,715 (98.22%) number of supplementary alignments = 808,593 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 181,362,260 number of mapped paired reads (second in pair) = 179,026,455 number of mapped paired reads (both in pair) = 356,690,572 number of mapped paired reads (singletons) = 3,698,143 number of mapped bases = 35,633,859,894 bp number of sequenced bases = 35,623,366,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,734,951 duplication rate = 9.36% >>>>>>> Insert size mean insert size = 37,021.2614 std insert size = 1,783,881.2311 median insert size = 308 >>>>>>> Mapping quality mean mapping quality = 53.7828 >>>>>>> ACTG content number of A's = 10,406,036,729 bp (29.21%) number of C's = 7,395,043,775 bp (20.76%) number of T's = 10,386,379,608 bp (29.16%) number of G's = 7,428,159,151 bp (20.85%) number of N's = 7,747,728 bp (0.02%) GC percentage = 41.61% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 222,061,962 number of insertions = 3,573,279 mapped reads with insertion percentage = 0.96% number of deletions = 4,283,283 mapped reads with deletion percentage = 1.16% homopolymer indels = 42.03% >>>>>>> Coverage mean coverageData = 11.5108X std coverageData = 126.4264X There is a 91.98% of reference with a coverageData >= 1X There is a 91.61% of reference with a coverageData >= 2X There is a 90.89% of reference with a coverageData >= 3X There is a 89.63% of reference with a coverageData >= 4X There is a 87.65% of reference with a coverageData >= 5X There is a 84.76% of reference with a coverageData >= 6X There is a 80.82% of reference with a coverageData >= 7X There is a 75.73% of reference with a coverageData >= 8X There is a 69.51% of reference with a coverageData >= 9X There is a 62.29% of reference with a coverageData >= 10X There is a 54.4% of reference with a coverageData >= 11X There is a 46.2% of reference with a coverageData >= 12X There is a 38.14% of reference with a coverageData >= 13X There is a 30.59% of reference with a coverageData >= 14X There is a 23.85% of reference with a coverageData >= 15X There is a 18.1% of reference with a coverageData >= 16X There is a 13.39% of reference with a coverageData >= 17X There is a 9.68% of reference with a coverageData >= 18X There is a 6.87% of reference with a coverageData >= 19X There is a 4.8% of reference with a coverageData >= 20X There is a 3.33% of reference with a coverageData >= 21X There is a 2.31% of reference with a coverageData >= 22X There is a 1.62% of reference with a coverageData >= 23X There is a 1.16% of reference with a coverageData >= 24X There is a 0.86% of reference with a coverageData >= 25X There is a 0.67% of reference with a coverageData >= 26X There is a 0.54% of reference with a coverageData >= 27X There is a 0.46% of reference with a coverageData >= 28X There is a 0.4% of reference with a coverageData >= 29X There is a 0.36% of reference with a coverageData >= 30X There is a 0.33% of reference with a coverageData >= 31X There is a 0.31% of reference with a coverageData >= 32X There is a 0.29% of reference with a coverageData >= 33X There is a 0.27% of reference with a coverageData >= 34X There is a 0.26% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2971388815 11.921289516065038 287.9931309622076 chr2 243199373 3100527942 12.748914208754972 80.13053407142809 chr3 198022430 2332741528 11.780188375629972 12.713823332087532 chr4 191154276 2308464499 12.076447084029656 88.16491422718029 chr5 180915260 2117636549 11.705129512015736 11.056594410254574 chr6 171115067 2033513326 11.883894046571598 47.96631771322698 chr7 159138663 1923863000 12.08922435147014 104.51191933863304 chr8 146364022 1769723597 12.091247376353186 70.57317401071178 chr9 141213431 1506550953 10.66860951066333 107.48067602017164 chr10 135534747 1971722777 14.547729055782279 330.81157171888526 chr11 135006516 1648111183 12.207641763009423 57.090040311858495 chr12 133851895 1588016662 11.863983412412653 10.131944630045108 chr13 115169878 1094130313 9.500143023508283 7.12606328425504 chr14 107349540 1083210047 10.090495469286594 10.120401094817295 chr15 102531392 1032204018 10.067199887425696 7.488448660873854 chr16 90354753 1165924761 12.903856435753855 90.42950216807961 chr17 81195210 1048682636 12.915572679718421 53.31841059964872 chr18 78077248 967165103 12.387284743949992 138.61301392894651 chr19 59128983 762143386 12.889506081983518 153.64608370173025 chr20 63025520 772938140 12.263891515690787 42.09901436441169 chr21 48129895 493801212 10.25976084094927 51.44243434594005 chr22 51304566 476943984 9.29632625680919 48.62458603490195 chrMT 16571 100881557 6087.837607869169 922.376330969766 chrX 155270560 925255406 5.958988014212095 22.00219319835814 chrY 59373566 438318500 7.382384612034251 127.70996350245451