BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084792.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 = 1,609,941 number of mapped reads = 1,437,042 (89.26%) number of supplementary alignments = 13,118 (0.81%) number of secondary alignments = 0 number of mapped bases = 96,295,001 bp number of sequenced bases = 96,256,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,609 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9558 >>>>>>> ACTG content number of A's = 26,950,813 bp (28%) number of C's = 18,099,584 bp (18.8%) number of T's = 29,956,805 bp (31.12%) number of G's = 21,217,560 bp (22.04%) number of N's = 31,690 bp (0.03%) GC percentage = 40.85% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 818,061 number of insertions = 7,534 mapped reads with insertion percentage = 0.52% number of deletions = 23,766 mapped reads with deletion percentage = 1.64% homopolymer indels = 46.81% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.2715X There is a 2.77% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7783504 0.03122762129447212 0.4364760727266331 chr2 243199373 8199719 0.033716036759683585 0.32709327711827096 chr3 198022430 6632109 0.033491705964824287 0.19911367430515012 chr4 191154276 5931686 0.03103088313860162 0.19886670057798922 chr5 180915260 5723219 0.031634805156845254 0.19568255736052598 chr6 171115067 5661524 0.033086063660308765 0.23184398014654742 chr7 159138663 5597143 0.03517148438026025 0.3069981023578364 chr8 146364022 4682379 0.031991325026583375 0.293364894971184 chr9 141213431 4063355 0.028774564651715035 0.2656602987429215 chr10 135534747 4435971 0.032729400380258206 0.2452904167450659 chr11 135006516 4447986 0.03294645422892033 0.2611129880431419 chr12 133851895 4287991 0.03203534025424145 0.19747363550165237 chr13 115169878 3303560 0.028684236341728172 0.18626412820466623 chr14 107349540 2920157 0.02720232429500862 0.19631943501222562 chr15 102531392 2832715 0.02762778252342463 0.18501856425699317 chr16 90354753 2814817 0.031152948865899727 0.21025243245582578 chr17 81195210 2683007 0.03304390739305927 0.22643272517218044 chr18 78077248 2500095 0.03202078792531212 0.5305582889654175 chr19 59128983 1822402 0.030820790541924253 0.34953966093133954 chr20 63025520 2016842 0.032000402376688046 0.20435455238082811 chr21 48129895 1232192 0.025601385583741663 0.1834042878749769 chr22 51304566 1065125 0.020760822730670793 0.15657846344513768 chrMT 16571 4977 0.3003439744131314 0.6384284250109155 chrX 155270560 5419170 0.03490146490100892 0.227183597942885 chrY 59373566 233356 0.003930301238770128 0.08812627552029863