BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818907.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 = 2,768,991 number of mapped reads = 2,643,172 (95.46%) number of supplementary alignments = 41,758 (1.51%) number of secondary alignments = 0 number of mapped bases = 244,706,776 bp number of sequenced bases = 244,547,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 731,024 duplication rate = 23.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1966 >>>>>>> ACTG content number of A's = 71,174,061 bp (29.1%) number of C's = 51,151,907 bp (20.92%) number of T's = 70,949,070 bp (29.01%) number of G's = 51,269,043 bp (20.96%) number of N's = 3,528 bp (0%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,491,659 number of insertions = 35,435 mapped reads with insertion percentage = 1.3% number of deletions = 81,453 mapped reads with deletion percentage = 3.01% homopolymer indels = 40.44% >>>>>>> Coverage mean coverageData = 0.079X std coverageData = 0.9447X There is a 4.93% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 24706828 0.09912443909216981 1.4753633976071732 chr2 243199373 18463353 0.07591858799734652 1.412695218301358 chr3 198022430 15306297 0.07729577401913511 0.40432825189384924 chr4 191154276 12378130 0.0647546592156798 0.512120430559883 chr5 180915260 10734401 0.0593338616101262 0.39203811218162776 chr6 171115067 12187613 0.07122466310929826 0.44206167046928035 chr7 159138663 21885496 0.13752469442325277 2.0483836482970785 chr8 146364022 21243621 0.14514236975532144 0.747938487413303 chr9 141213431 8815936 0.062429869011539 0.7494133043477987 chr10 135534747 11061646 0.08161483490281647 1.1952295702297548 chr11 135006516 10729592 0.07947462328410874 0.535208273218175 chr12 133851895 9445295 0.07056526917306624 0.392271159413083 chr13 115169878 7405818 0.06430342836692073 0.3621350488827414 chr14 107349540 7071259 0.06587134886651587 0.4142243666280588 chr15 102531392 6686535 0.06521451498483509 0.3691392812826914 chr16 90354753 5954270 0.06589880224673958 0.959266679832762 chr17 81195210 5890562 0.07254814662096447 0.5579374769593204 chr18 78077248 4710785 0.06033492625149903 0.9049396324908645 chr19 59128983 4088574 0.06914669917458245 1.2438324413310937 chr20 63025520 9941065 0.15773078905179996 0.6329701228558795 chr21 48129895 2284105 0.047457095013400716 0.3934024675520805 chr22 51304566 2142820 0.04176665289401337 0.3388186685544796 chrMT 16571 767334 46.305835495745576 27.041470865726954 chrX 155270560 9933613 0.06397615233692723 0.46386996914453055 chrY 59373566 871828 0.014683773583685373 1.1330544886936587