BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236075.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,556,160 number of mapped reads = 1,241,843 (79.8%) number of supplementary alignments = 8,952 (0.58%) number of secondary alignments = 0 number of mapped bases = 81,517,019 bp number of sequenced bases = 81,480,315 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,401 duplication rate = 6.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0348 >>>>>>> ACTG content number of A's = 22,173,629 bp (27.21%) number of C's = 14,440,239 bp (17.72%) number of T's = 26,577,163 bp (32.62%) number of G's = 18,247,954 bp (22.4%) number of N's = 41,330 bp (0.05%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 665,877 number of insertions = 6,094 mapped reads with insertion percentage = 0.49% number of deletions = 20,735 mapped reads with deletion percentage = 1.65% homopolymer indels = 48.92% >>>>>>> Coverage mean coverageData = 0.0263X std coverageData = 0.2857X There is a 1.93% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% 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 5739729 0.023027942626469927 0.4397848360587738 chr2 243199373 6462433 0.02657257261925589 0.2960076649054292 chr3 198022430 7548258 0.03811819701434832 0.2558059047022191 chr4 191154276 5428547 0.028398773564448018 0.2273462574043778 chr5 180915260 4880732 0.02697800063963648 0.21499325646222794 chr6 171115067 5446384 0.031828781038901736 0.25428841682310604 chr7 159138663 3907316 0.024552902018537128 0.2740027007014258 chr8 146364022 4735132 0.03235174830054889 0.4422199535771205 chr9 141213431 3677611 0.026042926469225156 0.2663631368752966 chr10 135534747 3261129 0.0240612025490408 0.259397158420259 chr11 135006516 3090901 0.02289445792379384 0.24034192253932055 chr12 133851895 3025500 0.02260334080440176 0.1993475514110275 chr13 115169878 2165860 0.01880578531132941 0.17858384372476135 chr14 107349540 2517109 0.02344778561696678 0.20853040343297805 chr15 102531392 2230870 0.02175792171045527 0.19202813672235394 chr16 90354753 1885229 0.020864746318325942 0.19442390608333707 chr17 81195210 3301544 0.040661807513029405 0.2839064971922177 chr18 78077248 1978830 0.025344515216519925 0.44986851290851626 chr19 59128983 1955132 0.033065544184989616 0.33806186834268187 chr20 63025520 1543111 0.02448390747113233 0.20778240986449417 chr21 48129895 1195868 0.024846677932706895 0.2131766273983777 chr22 51304566 944810 0.018415709822006875 0.1722653917312572 chrMT 16571 311123 18.775149357310966 12.044917941242641 chrX 155270560 4076543 0.026254449008234402 0.22769250280475814 chrY 59373566 207318 0.0034917559103659025 0.09767027146604436