BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230350.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 = 2,291,193 number of mapped reads = 1,822,330 (79.54%) number of supplementary alignments = 7,285 (0.32%) number of secondary alignments = 0 number of mapped bases = 116,803,666 bp number of sequenced bases = 116,756,829 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,385 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6607 >>>>>>> ACTG content number of A's = 30,536,331 bp (26.15%) number of C's = 19,988,864 bp (17.12%) number of T's = 38,955,601 bp (33.36%) number of G's = 27,061,392 bp (23.18%) number of N's = 214,641 bp (0.18%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,050,977 number of insertions = 9,845 mapped reads with insertion percentage = 0.54% number of deletions = 29,038 mapped reads with deletion percentage = 1.58% homopolymer indels = 48.32% >>>>>>> Coverage mean coverageData = 0.0377X std coverageData = 0.3451X There is a 3.14% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 7035474 0.02822650540156528 0.5310425586982802 chr2 243199373 11439214 0.047036363041939255 0.4585982572190301 chr3 198022430 7113301 0.035921693315247166 0.22033832946179124 chr4 191154276 6460762 0.03379867892675338 0.22397761010235043 chr5 180915260 7474289 0.0413137565067756 0.23559549012632472 chr6 171115067 5974416 0.03491461099682122 0.30160948827641115 chr7 159138663 5806169 0.03648496782959651 0.485567221258117 chr8 146364022 6160905 0.04209302884557244 0.3564754670525998 chr9 141213431 5744088 0.0406766407368149 0.37686695768232953 chr10 135534747 4293887 0.031681078801143146 0.2835234891556835 chr11 135006516 5780490 0.042816377840607336 0.3393379706447821 chr12 133851895 5237607 0.03912986812775419 0.23567464198082677 chr13 115169878 2588189 0.022472794492323766 0.17326593733559162 chr14 107349540 4901560 0.04565981372626282 0.2621849376262923 chr15 102531392 4137420 0.04035271461056532 0.23199807687291651 chr16 90354753 4308056 0.047679351190302074 0.2829760802660432 chr17 81195210 4839730 0.059606102379684715 0.3071068436949226 chr18 78077248 4773495 0.06113810517501846 0.6193435823532631 chr19 59128983 2536864 0.04290390044422039 0.4335553074107862 chr20 63025520 1261192 0.020010814666820677 0.17366330476181566 chr21 48129895 2004941 0.04165687458906777 0.25175595229940495 chr22 51304566 1706977 0.033271444104994476 0.21083581101604507 chrMT 16571 97578 5.888479874479512 6.238664882496735 chrX 155270560 4875713 0.031401400239684844 0.263036004050879 chrY 59373566 251349 0.00423334855784138 0.10551559966190778