BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085009.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 = 1,695,634 number of mapped reads = 1,526,900 (90.05%) number of supplementary alignments = 37,183 (2.19%) number of secondary alignments = 0 number of mapped bases = 105,988,376 bp number of sequenced bases = 105,951,433 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,821 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1741 >>>>>>> ACTG content number of A's = 31,937,502 bp (30.14%) number of C's = 19,733,909 bp (18.63%) number of T's = 31,832,128 bp (30.04%) number of G's = 22,432,919 bp (21.17%) number of N's = 14,975 bp (0.01%) GC percentage = 39.8% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 905,872 number of insertions = 10,008 mapped reads with insertion percentage = 0.65% number of deletions = 21,863 mapped reads with deletion percentage = 1.42% homopolymer indels = 44.53% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 0.4795X There is a 3.14% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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% 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 8368619 0.03357511795326681 1.0383307291845036 chr2 243199373 9067210 0.03728303197557997 0.44223782462733857 chr3 198022430 7229324 0.03650760168936418 0.22677015707747888 chr4 191154276 7276486 0.038066038344860255 0.21209568650801092 chr5 180915260 6611127 0.036542671966975034 0.2031508390363455 chr6 171115067 6341930 0.037062370434042494 0.3011333118288761 chr7 159138663 5831730 0.03664558875928221 0.4057255812839639 chr8 146364022 5561781 0.037999645841926916 0.7550818721119565 chr9 141213431 4442209 0.03145741144126723 0.39599496045028143 chr10 135534747 5181330 0.03822879456882005 0.6450220079002826 chr11 135006516 4830332 0.035778510127614876 0.3987837280800355 chr12 133851895 4718271 0.035249938000504216 0.20690096662867694 chr13 115169878 3484134 0.03025212894642469 0.1797494437111899 chr14 107349540 3175442 0.029580396897834867 0.23663174241492285 chr15 102531392 2820898 0.027512530016172997 0.17337017820747458 chr16 90354753 2716576 0.030065667934480435 0.26781311684198517 chr17 81195210 2436119 0.03000323541253234 0.24981742475958155 chr18 78077248 2979601 0.03816221852491522 0.9146448648784973 chr19 59128983 1770268 0.02993909095307795 0.7185510297625182 chr20 63025520 1949745 0.03093580187835023 0.19886260728671432 chr21 48129895 1362285 0.028304341823309608 0.208169954759698 chr22 51304566 923251 0.017995493812383093 0.1392129761448009 chrMT 16571 30949 1.867660370526824 1.751418386973674 chrX 155270560 6605162 0.0425396932940797 0.27344186449997127 chrY 59373566 273597 0.004608060765627586 0.10764539972453531