BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084778.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 = 2,430,148 number of mapped reads = 2,161,992 (88.97%) number of supplementary alignments = 23,307 (0.96%) number of secondary alignments = 0 number of mapped bases = 145,031,339 bp number of sequenced bases = 144,978,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,619 duplication rate = 3.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9989 >>>>>>> ACTG content number of A's = 40,680,073 bp (28.06%) number of C's = 26,759,928 bp (18.46%) number of T's = 45,803,482 bp (31.59%) number of G's = 31,678,251 bp (21.85%) number of N's = 56,481 bp (0.04%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,247,454 number of insertions = 10,971 mapped reads with insertion percentage = 0.5% number of deletions = 33,154 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.96% >>>>>>> Coverage mean coverageData = 0.0468X std coverageData = 0.335X There is a 3.9% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% 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 10970454 0.04401374791359096 0.4986135236710948 chr2 243199373 12846840 0.05282431381926301 0.40663347029085506 chr3 198022430 10486862 0.05295795026856301 0.266764260337667 chr4 191154276 9964775 0.0521294904226992 0.2763293626528423 chr5 180915260 9123771 0.05043118529636472 0.26117427901030416 chr6 171115067 8406961 0.049130454421059254 0.3067262163794004 chr7 159138663 8339289 0.05240265842876913 0.39351995882040186 chr8 146364022 7395639 0.050529077425871774 0.440494192015265 chr9 141213431 6155657 0.04359115812432884 0.318906599439776 chr10 135534747 6997586 0.051629461484146204 0.3222789542064418 chr11 135006516 6012898 0.04453783549232542 0.2858864741779331 chr12 133851895 6361588 0.047527067136404755 0.2559509618626879 chr13 115169878 4763994 0.041364930507263364 0.24052644598568984 chr14 107349540 4739783 0.044152802145216455 0.2544116168632985 chr15 102531392 4082159 0.03981374796901226 0.23730302990877103 chr16 90354753 3821712 0.04229674558459587 0.25239451715273115 chr17 81195210 3516234 0.04330592900738849 0.27673782488789783 chr18 78077248 3754882 0.048091884591014274 0.5613015180911234 chr19 59128983 2481835 0.041973240094455876 0.3778361438897929 chr20 63025520 2724864 0.04323429620255414 0.24847505072668796 chr21 48129895 1704279 0.03540998790876232 0.22597351700256457 chr22 51304566 1276094 0.024872912870951877 0.18013826766247165 chrMT 16571 14985 0.9042906282059019 1.0570308389692669 chrX 155270560 8750516 0.056356568817681855 0.29483056886601583 chrY 59373566 337682 0.0056874131494813705 0.10951144259488155