BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234061.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 = 5,270,566 number of mapped reads = 4,960,921 (94.13%) number of supplementary alignments = 52,287 (0.99%) number of secondary alignments = 0 number of mapped bases = 342,085,408 bp number of sequenced bases = 341,978,719 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 850,409 duplication rate = 6.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8748 >>>>>>> ACTG content number of A's = 86,751,895 bp (25.37%) number of C's = 58,969,046 bp (17.24%) number of T's = 93,627,934 bp (27.38%) number of G's = 102,554,939 bp (29.99%) number of N's = 74,905 bp (0.02%) GC percentage = 47.23% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 2,047,233 number of insertions = 22,130 mapped reads with insertion percentage = 0.44% number of deletions = 65,166 mapped reads with deletion percentage = 1.3% homopolymer indels = 47.57% >>>>>>> Coverage mean coverageData = 0.1105X std coverageData = 72.6298X There is a 5.8% of reference with a coverageData >= 1X There is a 2.24% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 51337484 0.20596732635623002 2.0512539910573344 chr2 243199373 72082956 0.29639449769469595 259.10486774494467 chr3 198022430 8728139 0.04407651698850479 0.31537330091808385 chr4 191154276 6396746 0.03346378712448996 0.29351591359612145 chr5 180915260 27689145 0.15305035628282546 0.5987538921234477 chr6 171115067 45561466 0.26626215212246623 1.124736489086314 chr7 159138663 6283610 0.039485124994420744 0.629485626307608 chr8 146364022 4558648 0.03114596017319065 1.293515707080865 chr9 141213431 5449719 0.03859207273279834 0.4993377568985975 chr10 135534747 12261913 0.09047062300562674 0.5902239741950864 chr11 135006516 5908245 0.04376266549978965 0.5033400284688282 chr12 133851895 3941236 0.0294447530981911 0.2665455824128419 chr13 115169878 37380081 0.32456473558129495 0.9122387650127334 chr14 107349540 3656444 0.03406110543184442 0.6900866544186357 chr15 102531392 3881280 0.037854552876839906 0.2898471845053623 chr16 90354753 9710986 0.10747620548528311 0.7817383244789532 chr17 81195210 8950286 0.11023169962858646 0.5639621050342809 chr18 78077248 4416667 0.05656791335678225 2.5072820663296866 chr19 59128983 4278865 0.07236493480701334 1.5049257190994905 chr20 63025520 2147449 0.03407268991989277 0.6603298262980484 chr21 48129895 4690134 0.09744741807560561 0.5023534292974424 chr22 51304566 1511676 0.02946474588636029 0.24866558614553672 chrMT 16571 46094 2.7816064208557116 2.798786051513467 chrX 155270560 10535917 0.06785521350602458 0.5397963610720035 chrY 59373566 680222 0.011456647222435654 0.20949268336970817