BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777298.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 1,395,970 number of mapped reads = 1,322,508 (94.74%) number of supplementary alignments = 44,010 (3.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 662,651 number of mapped paired reads (second in pair) = 659,857 number of mapped paired reads (both in pair) = 1,316,498 number of mapped paired reads (singletons) = 6,010 number of mapped bases = 127,982,067 bp number of sequenced bases = 127,932,298 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,062 duplication rate = 7.16% >>>>>>> Insert size mean insert size = 133,575.1893 std insert size = 3,490,384.2897 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 53.248 >>>>>>> ACTG content number of A's = 37,924,048 bp (29.64%) number of C's = 26,116,422 bp (20.41%) number of T's = 37,120,522 bp (29.02%) number of G's = 26,769,222 bp (20.92%) number of N's = 2,084 bp (0%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 719,235 number of insertions = 31,957 mapped reads with insertion percentage = 2.35% number of deletions = 18,356 mapped reads with deletion percentage = 1.34% homopolymer indels = 45.08% >>>>>>> Coverage mean coverageData = 0.0413X std coverageData = 0.5241X There is a 2.9% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% 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% 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 10443562 0.041899843451142296 0.9369432749587085 chr2 243199373 11262041 0.04630785376243548 0.45037127103728264 chr3 198022430 8688843 0.04387807482213 0.2890754724368489 chr4 191154276 8683196 0.045425068074333844 0.5134232485713031 chr5 180915260 7919366 0.043773897237856 0.2656797837941015 chr6 171115067 7194286 0.04204355657354241 0.29309111739357246 chr7 159138663 6741730 0.04236387231681091 0.3642576679253926 chr8 146364022 6678940 0.04563238908534503 0.36683919813593674 chr9 141213431 5355338 0.0379237156273046 0.46657944081476105 chr10 135534747 7683024 0.05668674764265432 1.3288357281989558 chr11 135006516 5961515 0.044157239047632336 0.2959379289141556 chr12 133851895 5644634 0.042170744015241624 0.26013125565144296 chr13 115169878 4041724 0.03509358584195079 0.23477520012201678 chr14 107349540 3812207 0.035512094416054324 0.24108607644694402 chr15 102531392 3528013 0.03440910077569219 0.23270039963287378 chr16 90354753 4122481 0.045625502401627945 0.5847204262540591 chr17 81195210 3089515 0.038050458887907306 0.30815149495823924 chr18 78077248 3501735 0.04484962123665014 0.5493461681394405 chr19 59128983 2081606 0.035204495230367824 0.5421161804781904 chr20 63025520 2710595 0.04300789584917348 0.28497495254918015 chr21 48129895 1684804 0.03500535374116233 0.2840747350153282 chr22 51304566 1227789 0.023931378739272445 0.19906942581349213 chrMT 16571 533974 32.223402329370586 9.32833876055046 chrX 155270560 3736875 0.024066861097171287 0.21122225048399945 chrY 59373566 1654274 0.02786212975653172 0.6055493491145835