BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082897.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 = 4,841,701 number of mapped reads = 4,214,147 (87.04%) number of supplementary alignments = 41,178 (0.85%) number of secondary alignments = 0 number of mapped bases = 286,943,788 bp number of sequenced bases = 286,837,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 230,485 duplication rate = 4.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4739 >>>>>>> ACTG content number of A's = 82,722,624 bp (28.84%) number of C's = 53,428,488 bp (18.63%) number of T's = 91,494,219 bp (31.9%) number of G's = 59,175,703 bp (20.63%) number of N's = 16,109 bp (0.01%) GC percentage = 39.26% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 2,559,406 number of insertions = 23,403 mapped reads with insertion percentage = 0.55% number of deletions = 61,947 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.97% >>>>>>> Coverage mean coverageData = 0.0927X std coverageData = 0.6246X There is a 6.71% of reference with a coverageData >= 1X There is a 1.7% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 27988164 0.11228924480793971 1.1155768913071644 chr2 243199373 29330454 0.12060250665202167 0.8753700001406804 chr3 198022430 23234953 0.11733495543913888 0.44348999576571574 chr4 191154276 12470175 0.06523618127171793 0.344008202030208 chr5 180915260 16163465 0.08934273979983778 0.3922023455850894 chr6 171115067 21679591 0.12669597937860141 0.6573439300392715 chr7 159138663 11024058 0.06927328527323369 0.5211636631740889 chr8 146364022 18281991 0.12490768393888492 0.7131448988248759 chr9 141213431 9590981 0.0679183341986783 0.5780394077402563 chr10 135534747 9267249 0.06837544766287866 0.4362857871882937 chr11 135006516 12589653 0.09325218791661878 0.5359757722909956 chr12 133851895 10016164 0.07483019945291025 0.3662845570201239 chr13 115169878 7632483 0.06627152110033493 0.3358108675605618 chr14 107349540 6838732 0.06370527530905117 0.3555711205354671 chr15 102531392 6305289 0.06149618060388764 0.3187703021839882 chr16 90354753 12171845 0.13471172900002285 0.5327897532734527 chr17 81195210 5826254 0.07175612945640512 0.4044060253253039 chr18 78077248 13529106 0.17327846903620372 1.2682494326510618 chr19 59128983 4997925 0.08452580691266075 0.8142157492466252 chr20 63025520 5034675 0.07988311718808508 0.3812738512592915 chr21 48129895 5885568 0.12228507874367896 0.4734835634998616 chr22 51304566 3940997 0.07681571655824941 0.3575505864969659 chrMT 16571 13591 0.8201677629593869 1.102697757929395 chrX 155270560 12669947 0.0815991582692817 0.4352337910794273 chrY 59373566 460478 0.007755606257505234 0.14628037986859166