BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046455.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 9,567,356 number of mapped reads = 9,528,680 (99.6%) number of supplementary alignments = 54,350 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,768,689 number of mapped paired reads (second in pair) = 4,759,991 number of mapped paired reads (both in pair) = 9,500,886 number of mapped paired reads (singletons) = 27,794 number of mapped bases = 930,564,578 bp number of sequenced bases = 930,325,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,449,799 duplication rate = 36.96% >>>>>>> Insert size mean insert size = 19,036.4557 std insert size = 1,359,043.0092 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 52.6165 >>>>>>> ACTG content number of A's = 272,582,188 bp (29.3%) number of C's = 193,454,650 bp (20.79%) number of T's = 273,256,267 bp (29.37%) number of G's = 190,951,136 bp (20.53%) number of N's = 81,597 bp (0.01%) GC percentage = 41.32% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 3,004,446 number of insertions = 77,191 mapped reads with insertion percentage = 0.8% number of deletions = 86,230 mapped reads with deletion percentage = 0.88% homopolymer indels = 47.48% >>>>>>> Coverage mean coverageData = 0.3006X std coverageData = 31.9922X There is a 2.58% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 156642180 0.6284525164733692 59.305607138139514 chr2 243199373 234816034 0.9655289448464162 56.2819357564468 chr3 198022430 19164065 0.09677724387080797 9.45823816288098 chr4 191154276 14147973 0.07401337441177618 6.2679288976338 chr5 180915260 57627179 0.31853133339885203 20.70045098211009 chr6 171115067 64338226 0.375993926940402 31.498177247362236 chr7 159138663 47778181 0.30022987562739545 27.638624238021325 chr8 146364022 98573502 0.673481779559187 55.10556539334161 chr9 141213431 8075665 0.05718765518840768 3.9613208306457524 chr10 135534747 9895922 0.07301391133301043 4.546874117296198 chr11 135006516 78365229 0.580455161142 60.05442814065268 chr12 133851895 11557361 0.08634439579656306 6.434141139818473 chr13 115169878 6511934 0.0565419892170069 3.8619092890120523 chr14 107349540 11292643 0.1051950758242653 9.071392766253478 chr15 102531392 7826487 0.07633259285117285 5.507641210779429 chr16 90354753 37912490 0.4195959674639363 27.288595106797484 chr17 81195210 8909825 0.10973338205541928 11.66252992506367 chr18 78077248 2862531 0.03666280604562292 1.4526323003902435 chr19 59128983 5936538 0.10039979886006158 5.523499147583772 chr20 63025520 7520982 0.11933232760316773 6.181693419914205 chr21 48129895 2028876 0.04215417465589734 4.469229309263506 chr22 51304566 1315406 0.025639160459909164 1.6197119394637292 chrMT 16571 56595 3.415303844064933 2.498218559982576 chrX 155270560 37253232 0.23992463220329727 23.76735126568668 chrY 59373566 155522 0.0026193811569276467 0.11362362268581164