BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089580.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 24,458,524 number of mapped reads = 21,230,032 (86.8%) number of supplementary alignments = 771 (0%) number of secondary alignments = 0 number of mapped bases = 998,717,374 bp number of sequenced bases = 998,518,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,343,603 duplication rate = 8.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.258 >>>>>>> ACTG content number of A's = 309,181,179 bp (30.96%) number of C's = 202,238,330 bp (20.25%) number of T's = 269,197,634 bp (26.96%) number of G's = 217,644,728 bp (21.8%) number of N's = 256,439 bp (0.03%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 4,259,744 number of insertions = 39,598 mapped reads with insertion percentage = 0.19% number of deletions = 132,120 mapped reads with deletion percentage = 0.62% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 0.3226X std coverageData = 1.6866X There is a 16.43% of reference with a coverageData >= 1X There is a 7.03% of reference with a coverageData >= 2X There is a 3.44% of reference with a coverageData >= 3X There is a 1.85% of reference with a coverageData >= 4X There is a 1.07% of reference with a coverageData >= 5X There is a 0.65% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% 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 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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% 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 81172547 0.32566637817925437 2.544016663638305 chr2 243199373 83917160 0.34505500143703083 1.834553911123914 chr3 198022430 67441556 0.3405753378544037 1.0328128965834937 chr4 191154276 64239705 0.3360620873581714 1.1473630121922855 chr5 180915260 61733824 0.3412306070809063 1.0510390926282311 chr6 171115067 60259248 0.352156294921709 1.3359270571208333 chr7 159138663 54325249 0.3413705254014859 2.364500212468343 chr8 146364022 48488120 0.33128441906303996 3.157394659935084 chr9 141213431 41537414 0.29414634079671925 1.4795471888972949 chr10 135534747 47740465 0.35223782872446724 1.703489638004433 chr11 135006516 45070898 0.3338423902443346 1.479819616446116 chr12 133851895 44063864 0.32919865647027263 1.0796054610936805 chr13 115169878 33221786 0.2884589840409486 0.9534686206418745 chr14 107349540 30051307 0.27993885209009745 1.1862291407428227 chr15 102531392 28871566 0.2815875746620118 0.9439340566129103 chr16 90354753 27797917 0.30765306834494915 1.1287589787029861 chr17 81195210 26357336 0.32461688318806 1.2274080527290174 chr18 78077248 25601578 0.3279006196529878 2.4704260045915594 chr19 59128983 19211671 0.32491123684640405 2.2683287539862955 chr20 63025520 20721982 0.328787164310584 1.1100901951300242 chr21 48129895 13025019 0.27062221930881003 1.1558734504110897 chr22 51304566 11020747 0.21481025684926366 0.8204370411581641 chrMT 16571 449297 27.113451209945083 20.581381210669495 chrX 155270560 59571070 0.3836597871483171 1.394609435639778 chrY 59373566 2826048 0.04759774745549223 0.7508720670744764