BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089730.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 21,127,005 number of mapped reads = 18,430,507 (87.24%) number of supplementary alignments = 98,283 (0.47%) number of secondary alignments = 0 number of mapped bases = 1,237,874,147 bp number of sequenced bases = 1,237,453,996 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,787,873 duplication rate = 13.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3175 >>>>>>> ACTG content number of A's = 333,961,582 bp (26.99%) number of C's = 236,644,116 bp (19.12%) number of T's = 381,465,099 bp (30.83%) number of G's = 283,652,280 bp (22.92%) number of N's = 1,730,919 bp (0.14%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 10,626,245 number of insertions = 84,549 mapped reads with insertion percentage = 0.45% number of deletions = 237,289 mapped reads with deletion percentage = 1.27% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.3999X std coverageData = 3.1402X There is a 11.35% of reference with a coverageData >= 1X There is a 7.07% of reference with a coverageData >= 2X There is a 4.94% of reference with a coverageData >= 3X There is a 3.61% of reference with a coverageData >= 4X There is a 2.7% of reference with a coverageData >= 5X There is a 2.05% of reference with a coverageData >= 6X There is a 1.58% of reference with a coverageData >= 7X There is a 1.22% of reference with a coverageData >= 8X There is a 0.95% of reference with a coverageData >= 9X There is a 0.74% of reference with a coverageData >= 10X There is a 0.59% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 100309472 0.40244422099152966 6.85004765364407 chr2 243199373 107204233 0.44080801557000726 3.4476295495428766 chr3 198022430 83958179 0.4239831770572657 1.7253202403098895 chr4 191154276 81198109 0.4247778846443383 2.0297430832768018 chr5 180915260 76775871 0.42437476529066703 1.739329872436281 chr6 171115067 71338338 0.4169027266313141 1.9962910652785324 chr7 159138663 66029028 0.4149150605846173 3.096215181048181 chr8 146364022 65618538 0.44832423366993834 4.508927187160765 chr9 141213431 50933294 0.36068307128661153 2.8255645610189433 chr10 135534747 57117638 0.42142431564062316 2.7624184921840045 chr11 135006516 57802759 0.42814791991225076 2.365761647936176 chr12 133851895 54414611 0.4065285067499418 1.8083284175250118 chr13 115169878 39117971 0.33965453189070843 1.5483253468223455 chr14 107349540 38319365 0.35695881882679703 1.7278723221792236 chr15 102531392 34829548 0.33969643170357033 1.646523523948998 chr16 90354753 34649426 0.38348205102170996 1.8142287324265527 chr17 81195210 30565488 0.37644447252491864 2.0034367103400585 chr18 78077248 33801055 0.43291811463436825 4.563055323360459 chr19 59128983 22804653 0.3856763949415467 4.007514652102175 chr20 63025520 26427311 0.4193112726400353 1.8545270069164523 chr21 48129895 15919287 0.3307567365355773 1.8496083645782078 chr22 51304566 13821889 0.26940855517616114 1.4399569127193637 chrMT 16571 54042 3.2612395148150384 4.733753576668253 chrX 155270560 71034675 0.4574896554762216 2.0424066593959025 chrY 59373566 3829367 0.06449615978935812 2.0844587226202225