BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080773.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 = 2,930,324 number of mapped reads = 2,629,152 (89.72%) number of supplementary alignments = 30,360 (1.04%) number of secondary alignments = 0 number of mapped bases = 177,199,635 bp number of sequenced bases = 177,136,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,855 duplication rate = 4.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7594 >>>>>>> ACTG content number of A's = 50,508,429 bp (28.51%) number of C's = 34,637,951 bp (19.55%) number of T's = 53,673,991 bp (30.3%) number of G's = 38,312,690 bp (21.63%) number of N's = 3,774 bp (0%) GC percentage = 41.18% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,355,829 number of insertions = 13,577 mapped reads with insertion percentage = 0.51% number of deletions = 39,455 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.0572X std coverageData = 0.5X There is a 4.31% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 22674733 0.09097162088916119 0.9529713003185154 chr2 243199373 13359299 0.05493146974519544 0.46181872229363147 chr3 198022430 10529677 0.05317416314909377 0.2879269620420786 chr4 191154276 10254901 0.05364724878035164 0.3079698597012613 chr5 180915260 14168895 0.07831785444743578 0.3522376092709387 chr6 171115067 12464650 0.07284367308227743 0.4805876184185439 chr7 159138663 12311088 0.07736076053372398 0.7358233568954744 chr8 146364022 7942663 0.05426649863447999 0.8842809212176144 chr9 141213431 6033324 0.04272485950716685 0.3361264514615369 chr10 135534747 7331607 0.0540939291383338 0.40591950264884985 chr11 135006516 7128866 0.05280386614820873 0.35900839043338334 chr12 133851895 6835642 0.05106869798145181 0.287217261891793 chr13 115169878 7333243 0.06367327227697506 0.320802777401824 chr14 107349540 4805741 0.044767224899147216 0.2779061045828834 chr15 102531392 4203357 0.040995805460243825 0.2546495517667293 chr16 90354753 4080482 0.04516067904031568 0.28278001002505854 chr17 81195210 4363127 0.05373626104298517 0.310258297635741 chr18 78077248 2348241 0.03007586794042741 0.6012343755104621 chr19 59128983 2741610 0.04636660163764359 0.6847932425776293 chr20 63025520 3115727 0.049435958640246046 0.29340669037149514 chr21 48129895 2899773 0.0602488952032827 0.32110754535785296 chr22 51304566 914623 0.017827321646186424 0.1615123791668563 chrMT 16571 166401 10.041699354293646 6.548527387154613 chrX 155270560 8761071 0.05642454693278623 0.3375579311724718 chrY 59373566 430894 0.007257337381419873 0.16057830735311476