BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867849.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 21,336,630 number of mapped reads = 20,918,738 (98.04%) number of supplementary alignments = 132,054 (0.62%) number of secondary alignments = 0 number of mapped bases = 1,881,788,586 bp number of sequenced bases = 1,881,274,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,175,387 duplication rate = 1.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.4357 >>>>>>> ACTG content number of A's = 531,109,983 bp (28.23%) number of C's = 401,992,651 bp (21.37%) number of T's = 534,979,287 bp (28.44%) number of G's = 413,135,114 bp (21.96%) number of N's = 57,925 bp (0%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 9,129,790 number of insertions = 198,302 mapped reads with insertion percentage = 0.93% number of deletions = 198,724 mapped reads with deletion percentage = 0.92% homopolymer indels = 35.96% >>>>>>> Coverage mean coverageData = 0.6079X std coverageData = 7.442X There is a 41.06% of reference with a coverageData >= 1X There is a 12.53% of reference with a coverageData >= 2X There is a 3.15% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171105417 0.6864794009881323 13.469703620448865 chr2 243199373 159825272 0.6571779771817092 4.736804932248052 chr3 198022430 116772694 0.5896942785723819 4.7167428343980875 chr4 191154276 106091954 0.5550069620205619 6.042953763016641 chr5 180915260 109883483 0.6073754253787105 0.9542512129986802 chr6 171115067 108139197 0.6319677097750837 2.009981423816965 chr7 159138663 104198233 0.6547637829532349 4.363524216736921 chr8 146364022 118898852 0.8123502646025947 3.980857668236623 chr9 141213431 73985537 0.5239270547856032 3.2758854870708776 chr10 135534747 105574693 0.7789492756422086 25.028031853731132 chr11 135006516 91546865 0.6780921966758997 2.3686194406566576 chr12 133851895 72158887 0.539094997497047 0.9381842942480247 chr13 115169878 51053869 0.44329185622650397 0.7437244904468081 chr14 107349540 46148019 0.42988557752553014 1.0218378167896516 chr15 102531392 51629532 0.5035485327264454 0.8083336905439474 chr16 90354753 64411756 0.7128762335280802 5.550554571750919 chr17 81195210 51063414 0.6288968770448404 1.9952408537425224 chr18 78077248 48981537 0.6273471242224111 6.413995546949795 chr19 59128983 41742539 0.7059573306038428 8.131772074226758 chr20 63025520 39789440 0.6313226769092901 1.8819930341329438 chr21 48129895 22418893 0.46579974878399383 4.295537279006927 chr22 51304566 31775632 0.6193529051585779 0.9999222286086716 chrMT 16571 1125359 67.91135115563334 22.12386273847692 chrX 155270560 84679315 0.5453661982026728 1.6751173956100347 chrY 59373566 8788197 0.1480153137509039 7.891030968982051