BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818927.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 = 3,057,787 number of mapped reads = 2,993,676 (97.9%) number of supplementary alignments = 44,289 (1.45%) number of secondary alignments = 0 number of mapped bases = 277,495,765 bp number of sequenced bases = 277,344,325 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,578,516 duplication rate = 43.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1775 >>>>>>> ACTG content number of A's = 78,061,650 bp (28.15%) number of C's = 59,352,980 bp (21.4%) number of T's = 82,152,627 bp (29.62%) number of G's = 57,764,540 bp (20.83%) number of N's = 12,528 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,751,152 number of insertions = 37,891 mapped reads with insertion percentage = 1.23% number of deletions = 85,584 mapped reads with deletion percentage = 2.81% homopolymer indels = 42% >>>>>>> Coverage mean coverageData = 0.0896X std coverageData = 0.8951X There is a 3.42% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 1.2% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 33267321 0.13346936054373962 1.488726175601204 chr2 243199373 24329108 0.10003770856761214 1.273420825544222 chr3 198022430 18862608 0.09525490622451205 0.6446276264410284 chr4 191154276 17263318 0.09031091724048067 0.6843164256486071 chr5 180915260 14281332 0.07893934430959555 0.5951840060291042 chr6 171115067 14834932 0.0866956502433535 0.6683561111227623 chr7 159138663 14248555 0.08953547008246512 0.8257232440014151 chr8 146364022 18169251 0.12413741267645678 0.8626985735835827 chr9 141213431 10011356 0.07089521109362466 0.9530668703430363 chr10 135534747 13504063 0.09963543149565919 1.0690793904347224 chr11 135006516 10403310 0.07705783623066016 0.678715548006058 chr12 133851895 12524599 0.09357057664368518 0.6559884612320244 chr13 115169878 4551027 0.03951577512307515 0.409147746221341 chr14 107349540 8385198 0.07811116843164861 0.6528810464081499 chr15 102531392 8081795 0.07882263999692894 0.5945619692854855 chr16 90354753 8136899 0.09005501902041611 0.9191299142038704 chr17 81195210 5885664 0.07248782286541287 0.6288629253126481 chr18 78077248 6932371 0.08878861867672386 1.17383607325216 chr19 59128983 4406586 0.07452497534077324 1.2436657348374285 chr20 63025520 5811146 0.09220306314013751 0.6822802178132407 chr21 48129895 3517163 0.07307647357219457 0.6207439047747515 chr22 51304566 3284245 0.06401467269014613 0.5792477212621457 chrMT 16571 88586 5.345845151167703 5.934363351564798 chrX 155270560 15941845 0.10267139501525595 0.770816486544827 chrY 59373566 773487 0.013027464107512087 0.7325774598289178