BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708602.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 5,280,159 number of mapped reads = 5,181,642 (98.13%) number of supplementary alignments = 179 (0%) number of secondary alignments = 0 number of mapped bases = 258,431,040 bp number of sequenced bases = 258,408,398 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,489 duplication rate = 1.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6902 >>>>>>> ACTG content number of A's = 80,071,676 bp (30.99%) number of C's = 48,940,577 bp (18.94%) number of T's = 79,706,910 bp (30.85%) number of G's = 49,680,162 bp (19.23%) number of N's = 9,073 bp (0%) GC percentage = 38.16% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 377,078 number of insertions = 16,328 mapped reads with insertion percentage = 0.31% number of deletions = 13,268 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.5% >>>>>>> Coverage mean coverageData = 0.0835X std coverageData = 0.3029X There is a 7.66% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 20013310 0.08029392231684751 0.29901783722920566 chr2 243199373 23309303 0.09584442061863375 0.3227075007753126 chr3 198022430 20428812 0.10316413145722937 0.3350541382976214 chr4 191154276 20238725 0.10587639169526085 0.3392216891556517 chr5 180915260 17533480 0.09691542880351829 0.3243921984540551 chr6 171115067 17342975 0.1013527055452107 0.33240733549538637 chr7 159138663 13558612 0.08519998688188049 0.3053773478269271 chr8 146364022 13550030 0.09257760079864435 0.3172346299400591 chr9 141213431 10964601 0.07764559590652535 0.2930508027345742 chr10 135534747 10373674 0.07653885243169414 0.288192590610235 chr11 135006516 11481974 0.08504755429730518 0.30620017099484714 chr12 133851895 12355980 0.09231083355226312 0.31857745472275417 chr13 115169878 9460475 0.08214365738930451 0.30056791198080623 chr14 107349540 8315144 0.07745858994831277 0.29311507453269875 chr15 102531392 6468216 0.06308522564484446 0.2647123737072753 chr16 90354753 4740422 0.05246455601511079 0.23958265979603707 chr17 81195210 4587879 0.05650430610377139 0.24921701512274863 chr18 78077248 7657372 0.09807430712721842 0.3262979360662886 chr19 59128983 2151749 0.03639076626770327 0.1979040674609725 chr20 63025520 4046349 0.0642017550985696 0.26497706258460935 chr21 48129895 3219526 0.06689243764192712 0.2739869530409722 chr22 51304566 1549218 0.030196493622029665 0.18179087256670082 chrMT 16571 500 0.03017319413433106 0.1710636504055231 chrX 155270560 14729218 0.09486162734262052 0.3219981860163872 chrY 59373566 353496 0.0059537606348252685 0.08111065435024073