BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084359.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 = 2,458,781 number of mapped reads = 2,226,512 (90.55%) number of supplementary alignments = 13,851 (0.56%) number of secondary alignments = 0 number of mapped bases = 149,423,038 bp number of sequenced bases = 149,372,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,697 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9612 >>>>>>> ACTG content number of A's = 41,447,081 bp (27.75%) number of C's = 28,820,499 bp (19.29%) number of T's = 45,837,284 bp (30.69%) number of G's = 33,066,915 bp (22.14%) number of N's = 201,207 bp (0.13%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,472,539 number of insertions = 10,342 mapped reads with insertion percentage = 0.46% number of deletions = 28,776 mapped reads with deletion percentage = 1.28% homopolymer indels = 46.29% >>>>>>> Coverage mean coverageData = 0.0483X std coverageData = 0.3366X There is a 4.05% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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% 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 14505262 0.05819548991213948 0.5437446357173807 chr2 243199373 14302631 0.05881031198217768 0.3717617248645721 chr3 198022430 9719422 0.0490824297025342 0.2563265676295625 chr4 191154276 8042490 0.04207329372009444 0.24228724860139514 chr5 180915260 7403995 0.04092520995741321 0.23249414847540872 chr6 171115067 7257866 0.042415119412015305 0.2628154992188367 chr7 159138663 8488341 0.05333927557252382 0.5252115309037337 chr8 146364022 7216965 0.04930832660501773 0.31308918540575476 chr9 141213431 5325896 0.0377152227113581 0.27091582893297783 chr10 135534747 10563656 0.07794057416139936 0.43344828813588876 chr11 135006516 8334404 0.06173334626307963 0.34739623770485123 chr12 133851895 7524950 0.05621847938723617 0.2729320789152772 chr13 115169878 3655807 0.03174273571775425 0.20500836696332198 chr14 107349540 3901020 0.03633941980561817 0.22351396267510815 chr15 102531392 3290066 0.03208837738202169 0.20945750621716858 chr16 90354753 3203360 0.03545314323420263 0.23146937500999568 chr17 81195210 4184992 0.05154235083572048 0.2748441793401233 chr18 78077248 4001821 0.05125463694622023 0.40457099409330965 chr19 59128983 3061316 0.051773527036648004 0.388081462128959 chr20 63025520 3015693 0.04784876031169596 0.2538504135611418 chr21 48129895 1415206 0.029403887126701608 0.2067511349065736 chr22 51304566 1260942 0.024577578533653322 0.17891264725385206 chrMT 16571 278657 16.81594351578058 9.965200259704677 chrX 155270560 9159561 0.05899097034234951 0.30654238487037894 chrY 59373566 308719 0.0051996034733706245 0.10989233042828682