BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472572.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 7,304,564 number of mapped reads = 6,717,702 (91.97%) number of supplementary alignments = 228,067 (3.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,384,502 number of mapped paired reads (second in pair) = 3,333,200 number of mapped paired reads (both in pair) = 6,563,194 number of mapped paired reads (singletons) = 154,508 number of mapped bases = 541,455,663 bp number of sequenced bases = 541,223,369 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,059,107 duplication rate = 14.04% >>>>>>> Insert size mean insert size = 243,226.9437 std insert size = 4,769,818.8281 median insert size = 122 >>>>>>> Mapping quality mean mapping quality = 50.213 >>>>>>> ACTG content number of A's = 139,495,373 bp (25.77%) number of C's = 109,525,504 bp (20.24%) number of T's = 159,688,582 bp (29.51%) number of G's = 132,154,779 bp (24.42%) number of N's = 359,131 bp (0.07%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 6,425,268 number of insertions = 52,629 mapped reads with insertion percentage = 0.77% number of deletions = 122,392 mapped reads with deletion percentage = 1.78% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.1749X std coverageData = 1.696X There is a 10.06% of reference with a coverageData >= 1X There is a 4.43% of reference with a coverageData >= 2X There is a 1.34% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 34965534 0.14028263544426636 2.2068643143639584 chr2 243199373 54644130 0.22468861381480618 2.360797679910398 chr3 198022430 28783217 0.14535331679345617 0.5521189474260184 chr4 191154276 27403437 0.14335769815580793 0.9828010750416593 chr5 180915260 25274864 0.1397055394884876 0.5730566345233714 chr6 171115067 35331395 0.20647740505516093 0.9457168173588907 chr7 159138663 45334702 0.2848754736616079 3.1897959530965987 chr8 146364022 25979972 0.17750244660535497 1.5331158697225598 chr9 141213431 19094895 0.13522010523205827 1.7868406437143967 chr10 135534747 21104661 0.15571402512744573 1.6267002751213262 chr11 135006516 19759831 0.14636205411004014 1.2793332451617552 chr12 133851895 27535639 0.20571721453775457 0.6835080472010012 chr13 115169878 25615792 0.2224174623159712 0.7157986417015815 chr14 107349540 13971446 0.13014909984709763 3.4374708599269583 chr15 102531392 12990928 0.12670195680167884 0.5243968419643057 chr16 90354753 19959838 0.2209052356105716 1.038459853054949 chr17 81195210 21471796 0.2644465849648027 1.4366624677419555 chr18 78077248 12201059 0.15626907085659578 3.164155303929198 chr19 59128983 11747745 0.19867997729641315 1.627849341132114 chr20 63025520 18783815 0.2980350657955698 1.0509319159447503 chr21 48129895 8285072 0.17213983117976883 0.7814950844769303 chr22 51304566 6088807 0.11867963175051514 0.5128698993903139 chrMT 16571 17502 1.0561824874781245 4.046099097690612 chrX 155270560 23819622 0.1534072009529688 0.8124446765346071 chrY 59373566 1289964 0.02172623419654464 0.8085275665695536