BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818930.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,142,877 number of mapped reads = 1,104,220 (96.62%) number of supplementary alignments = 15,453 (1.35%) number of secondary alignments = 0 number of mapped bases = 102,230,667 bp number of sequenced bases = 102,174,472 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 350,414 duplication rate = 28.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0899 >>>>>>> ACTG content number of A's = 29,327,654 bp (28.7%) number of C's = 21,200,877 bp (20.75%) number of T's = 29,850,048 bp (29.21%) number of G's = 21,791,690 bp (21.33%) number of N's = 4,203 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 655,598 number of insertions = 14,094 mapped reads with insertion percentage = 1.24% number of deletions = 31,012 mapped reads with deletion percentage = 2.75% homopolymer indels = 42.53% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.3852X There is a 1.96% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 11130627 0.04465636617210274 0.5453314685759119 chr2 243199373 9243163 0.03800652479478226 0.6220571119178554 chr3 198022430 6905459 0.03487210514485657 0.28274571457728404 chr4 191154276 7105720 0.03717269709415237 0.30920328348689124 chr5 180915260 5473497 0.03025447936232687 0.26862969740573045 chr6 171115067 5440585 0.03179489156264655 0.2844009171170408 chr7 159138663 5105546 0.03208237334506197 0.32962870828862734 chr8 146364022 6920107 0.0472801095886802 0.37797861061892385 chr9 141213431 3688139 0.02611748028415229 0.4111318151053669 chr10 135534747 4820434 0.03556603827946792 0.4334490686908356 chr11 135006516 3965555 0.029373063741604886 0.2912757754512821 chr12 133851895 4733104 0.03536075451154427 0.290049652931792 chr13 115169878 1655390 0.01437346317237568 0.18014153633139862 chr14 107349540 2088861 0.01945849977559289 0.24626681430320876 chr15 102531392 3060563 0.02985000925375128 0.26624125310851054 chr16 90354753 3041440 0.03366109583631976 0.42568074235203074 chr17 81195210 2134703 0.026290996722589915 0.2601680272688516 chr18 78077248 2504849 0.03208167634187106 0.5184584896028688 chr19 59128983 1539814 0.02604161143782906 0.49860969867301985 chr20 63025520 2165473 0.034358669313636764 0.29067139935640035 chr21 48129895 1327437 0.027580301182871893 0.2664701230426955 chr22 51304566 1205372 0.023494439071953168 0.2539066963010975 chrMT 16571 258231 15.583308189004889 10.652488621583355 chrX 155270560 6396192 0.041193848982060736 0.36776917770042394 chrY 59373566 320406 0.00539644191154023 0.30602972064280437