BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080959.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 = 5,582,035 number of mapped reads = 4,893,865 (87.67%) number of supplementary alignments = 53,458 (0.96%) number of secondary alignments = 0 number of mapped bases = 327,978,620 bp number of sequenced bases = 327,855,576 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 383,749 duplication rate = 6.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9818 >>>>>>> ACTG content number of A's = 92,088,083 bp (28.09%) number of C's = 57,315,072 bp (17.48%) number of T's = 107,315,331 bp (32.73%) number of G's = 70,488,838 bp (21.5%) number of N's = 648,252 bp (0.2%) GC percentage = 38.98% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 3,286,486 number of insertions = 26,376 mapped reads with insertion percentage = 0.53% number of deletions = 74,504 mapped reads with deletion percentage = 1.51% homopolymer indels = 49.36% >>>>>>> Coverage mean coverageData = 0.1059X std coverageData = 0.7493X There is a 7.26% of reference with a coverageData >= 1X There is a 2.14% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 27000981 0.10832864083415865 1.2231624472422575 chr2 243199373 21999262 0.09045772498763803 0.6472041698537494 chr3 198022430 29016448 0.14653111771227129 0.5206775497117692 chr4 191154276 20652366 0.1080403035294905 0.476155426804585 chr5 180915260 19119727 0.10568332931119244 0.44114025038365934 chr6 171115067 28307486 0.16542953520276504 0.79541663810491 chr7 159138663 16449321 0.1033647052822104 0.7120043710551611 chr8 146364022 25751905 0.17594422897178927 1.549768603329749 chr9 141213431 17015114 0.1204921789627787 0.8567140761574107 chr10 135534747 14609034 0.10778810838817592 0.6311087756911998 chr11 135006516 14778617 0.10946595348034906 0.5693150867561789 chr12 133851895 16312811 0.12187209602075488 0.4973423979767156 chr13 115169878 8806509 0.07646538446450382 0.37162741811797423 chr14 107349540 9018604 0.08401157564345409 0.5048501638159917 chr15 102531392 8049573 0.07850837526910782 0.3765366900116562 chr16 90354753 7010150 0.07758473978673817 0.47123052491949985 chr17 81195210 6169526 0.07598386653596931 0.39213225148124453 chr18 78077248 8149442 0.1043766552837518 1.4148702428869016 chr19 59128983 5907884 0.09991519725614087 0.9094458970537738 chr20 63025520 5052110 0.08015975116111695 0.409336929731649 chr21 48129895 6077571 0.12627434570551213 0.5778431239819434 chr22 51304566 2594148 0.050563686670695156 0.29734210741295974 chrMT 16571 34887 2.105304447528815 2.003877973230813 chrX 155270560 9373228 0.0603670650765992 0.38028663664371387 chrY 59373566 721916 0.012158878919282025 0.23852360028563138