BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818793.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 529,928 number of mapped reads = 516,137 (97.4%) number of supplementary alignments = 3,426 (0.65%) number of secondary alignments = 0 number of mapped bases = 35,101,337 bp number of sequenced bases = 35,086,872 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,972 duplication rate = 18.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8279 >>>>>>> ACTG content number of A's = 9,905,894 bp (28.23%) number of C's = 7,170,294 bp (20.44%) number of T's = 9,920,584 bp (28.27%) number of G's = 8,088,378 bp (23.05%) number of N's = 1,722 bp (0%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 179,365 number of insertions = 4,896 mapped reads with insertion percentage = 0.94% number of deletions = 8,847 mapped reads with deletion percentage = 1.7% homopolymer indels = 39.07% >>>>>>> Coverage mean coverageData = 0.0113X std coverageData = 0.1654X There is a 0.83% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.06% 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% 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 2896746 0.011621820593177177 0.21949953403090583 chr2 243199373 3154943 0.012972660912246678 0.24012697832812427 chr3 198022430 2555365 0.012904421988963573 0.14738471433280134 chr4 191154276 2243280 0.011735442423479975 0.14805703659547115 chr5 180915260 2170844 0.011999231021197439 0.14321686341876977 chr6 171115067 2059985 0.012038595058376712 0.1499532499846324 chr7 159138663 1881720 0.011824404984475708 0.154627700989643 chr8 146364022 1809117 0.012360394141123015 0.15165970944975538 chr9 141213431 1490230 0.010553033018509407 0.14115326641613382 chr10 135534747 1661335 0.01225763161678385 0.16918461789735983 chr11 135006516 1654269 0.012253253020765308 0.15045577332130028 chr12 133851895 1540244 0.011507076534105102 0.14118820626235945 chr13 115169878 1135416 0.009858619456035196 0.1297703646177071 chr14 107349540 1106119 0.010303900696733308 0.13972461590266144 chr15 102531392 988432 0.00964028655731115 0.12687054972700312 chr16 90354753 1015214 0.011235867138057475 0.17054208288596542 chr17 81195210 951454 0.011718105045851843 0.14518702757540947 chr18 78077248 948392 0.012146842060826734 0.1709815563238784 chr19 59128983 704130 0.011908373259184925 0.19277959312236156 chr20 63025520 730181 0.011585481563658658 0.1464813285011843 chr21 48129895 488840 0.010156681206140175 0.1372505081799739 chr22 51304566 430365 0.008388434666809188 0.12486873065272933 chrMT 16571 89143 5.3794580894333475 5.245059140843694 chrX 155270560 1070867 0.006896780690428372 0.1111221115822829 chrY 59373566 324706 0.005468864713296823 0.21021201491722105