BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080909.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,339,628 number of mapped reads = 2,994,355 (89.66%) number of supplementary alignments = 38,251 (1.15%) number of secondary alignments = 0 number of mapped bases = 207,412,844 bp number of sequenced bases = 207,337,839 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,213 duplication rate = 3.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.09 >>>>>>> ACTG content number of A's = 60,666,963 bp (29.26%) number of C's = 36,655,286 bp (17.68%) number of T's = 66,598,976 bp (32.12%) number of G's = 42,430,999 bp (20.46%) number of N's = 985,615 bp (0.48%) GC percentage = 38.14% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 2,364,466 number of insertions = 15,882 mapped reads with insertion percentage = 0.53% number of deletions = 45,722 mapped reads with deletion percentage = 1.51% homopolymer indels = 50.07% >>>>>>> Coverage mean coverageData = 0.067X std coverageData = 0.4407X There is a 4.78% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 15818041 0.06346239354003455 0.5691107437174693 chr2 243199373 17845951 0.07337992191287435 0.4394166952405569 chr3 198022430 14827928 0.07488004262951424 0.3615698910852275 chr4 191154276 14886877 0.07787885948206567 0.3781172178516788 chr5 180915260 13435776 0.07426557604925091 0.3603503147197592 chr6 171115067 12104563 0.07073931718707155 0.4056047338138826 chr7 159138663 11411561 0.07170828750773155 0.47458216401590425 chr8 146364022 11307316 0.07725475048779405 0.8989786048751975 chr9 141213431 9016923 0.0638531543079638 0.3921426331059763 chr10 135534747 9605239 0.07086919932052553 0.4121757075600622 chr11 135006516 9486018 0.0702634086194773 0.39746530041479095 chr12 133851895 9038287 0.06752453523351314 0.3447161908608793 chr13 115169878 7356847 0.063878221699601 0.3350827383941609 chr14 107349540 6163892 0.05741889532083696 0.3242663846340556 chr15 102531392 5714438 0.05573354548819546 0.3099566058777975 chr16 90354753 4976700 0.055079559566722516 0.31724850632380763 chr17 81195210 4293362 0.05287703548029496 0.31455903307937305 chr18 78077248 5702008 0.07303034041363753 0.6133385394715257 chr19 59128983 2628926 0.04446086955359946 0.4201088000884324 chr20 63025520 3622287 0.05747333778444033 0.32312964758167345 chr21 48129895 2761938 0.057385082597832385 0.32779247314967574 chr22 51304566 1845169 0.03596500553186631 0.24564082372309062 chrMT 16571 42525 2.5662301611248566 2.396069642944359 chrX 155270560 13101704 0.08437983349837858 0.402072962893506 chrY 59373566 418568 0.0070497365780589965 0.13398352790304852