BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081967.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,131,519 number of mapped reads = 2,874,647 (91.8%) number of supplementary alignments = 19,777 (0.63%) number of secondary alignments = 0 number of mapped bases = 196,974,544 bp number of sequenced bases = 196,901,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,066 duplication rate = 3.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0809 >>>>>>> ACTG content number of A's = 56,623,068 bp (28.76%) number of C's = 36,415,200 bp (18.49%) number of T's = 61,879,548 bp (31.43%) number of G's = 41,958,160 bp (21.31%) number of N's = 25,341 bp (0.01%) GC percentage = 39.8% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,523,351 number of insertions = 14,145 mapped reads with insertion percentage = 0.49% number of deletions = 41,624 mapped reads with deletion percentage = 1.43% homopolymer indels = 48.13% >>>>>>> Coverage mean coverageData = 0.0636X std coverageData = 0.556X There is a 5.38% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 18192860 0.07299022938041146 1.0705701109982053 chr2 243199373 17364703 0.07140110102175305 0.6819312388175013 chr3 198022430 12629015 0.0637756793510715 0.28988156945804305 chr4 191154276 10253442 0.05363961620194151 0.2819208598719803 chr5 180915260 9801594 0.05417781783581993 0.2665927340613208 chr6 171115067 17221876 0.10064500047795323 0.473219327634934 chr7 159138663 13085690 0.08222822633617326 0.7461627832551249 chr8 146364022 11323848 0.07736770174298709 0.8296221327849755 chr9 141213431 9661888 0.06842046065717361 0.5361597992066132 chr10 135534747 8011330 0.05910904898800601 0.5793149883349025 chr11 135006516 8818899 0.06532202490137587 0.38410883956104225 chr12 133851895 7843671 0.058599626101670056 0.28780997896126803 chr13 115169878 5391146 0.04681038213828793 0.2439672349979427 chr14 107349540 4897846 0.04562521646576222 0.27363455520701285 chr15 102531392 4493852 0.043829035306572256 0.23958381654327002 chr16 90354753 4205382 0.04654300809167172 0.3093047307236472 chr17 81195210 5207625 0.06413709626466882 0.3138479446812055 chr18 78077248 5683158 0.0727889128469282 0.90583174429624 chr19 59128983 3993206 0.06753381839833099 0.756462180855196 chr20 63025520 5005009 0.0794124189693318 0.3258281764867563 chr21 48129895 2122495 0.044099306678312925 0.27452828990998857 chr22 51304566 1546139 0.030136479470462725 0.19226555130456086 chrMT 16571 127938 7.720596222316094 4.638607841412606 chrX 155270560 9671493 0.06228800231028986 0.33529701050740146 chrY 59373566 420439 0.007081248918079133 0.16118955320735867