BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548959.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,258,775 number of mapped reads = 5,415,130 (86.52%) number of secondary alignments = 0 number of mapped bases = 214,778,201 bp number of sequenced bases = 214,756,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 219,480 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9299 >>>>>>> ACTG content number of A's = 61,551,727 bp (28.66%) number of C's = 45,618,414 bp (21.24%) number of T's = 61,981,255 bp (28.86%) number of G's = 45,605,043 bp (21.24%) number of N's = 299 bp (0%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0023 number of mismatches = 481,383 number of insertions = 5,597 mapped reads with insertion percentage = 0.1% number of deletions = 15,963 mapped reads with deletion percentage = 0.29% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 0.0694X std coverageData = 0.8149X There is a 5.44% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 17537164 0.07035955990657292 0.9812480952258187 chr2 243199373 18307948 0.07527958552754986 0.42237898562262305 chr3 198022430 14650859 0.07398585604671147 0.33083002124007144 chr4 191154276 13859285 0.07250313877362596 0.3428532859562354 chr5 180915260 13369528 0.07389939356138338 0.33440069409028167 chr6 171115067 12656336 0.07396389004131354 0.3463299515959941 chr7 159138663 12124740 0.0761897817377038 0.6723661383715398 chr8 146364022 11399636 0.077885506589864 3.0562269370807407 chr9 141213431 9228533 0.06535166615985699 0.3927693798499221 chr10 135534747 10248720 0.07561691910636023 0.4218090510294067 chr11 135006516 9862943 0.07305531090069756 0.41532052617297366 chr12 133851895 9894426 0.07392070168300569 0.3401551270010882 chr13 115169878 7067424 0.061365212178135675 0.2992956128252109 chr14 107349540 6819537 0.06352646690428296 0.33435719149029497 chr15 102531392 6405758 0.062476065866734744 0.3029217311811612 chr16 90354753 6233894 0.06899353706384434 0.33543438753940824 chr17 81195210 5847144 0.07201341064331258 0.3350086988933202 chr18 78077248 5769232 0.07389133387488248 0.6550831551093618 chr19 59128983 4308590 0.0728676493556468 0.7608757777316604 chr20 63025520 4673974 0.07416002279711456 0.3429755394044788 chr21 48129895 2829265 0.0587839429111574 0.34683547636132106 chr22 51304566 2673747 0.05211518600508189 0.35192482137919673 chrMT 16571 12147 0.7330275782994388 1.184846389046255 chrX 155270560 6892880 0.04439270393563339 0.30177410869198845 chrY 59373566 2104491 0.03544491499803128 0.4267990467261144