BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819086.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 = 880,322 number of mapped reads = 811,355 (92.17%) number of supplementary alignments = 3,248 (0.37%) number of secondary alignments = 0 number of mapped bases = 47,979,868 bp number of sequenced bases = 47,964,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,931 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.069 >>>>>>> ACTG content number of A's = 12,856,730 bp (26.8%) number of C's = 9,148,891 bp (19.07%) number of T's = 14,459,655 bp (30.15%) number of G's = 11,498,471 bp (23.97%) number of N's = 761 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 240,889 number of insertions = 3,823 mapped reads with insertion percentage = 0.47% number of deletions = 9,228 mapped reads with deletion percentage = 1.13% homopolymer indels = 41.65% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 0.1675X There is a 1.45% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4495687 0.018036813637467328 0.2862362706439716 chr2 243199373 3431947 0.014111660559256459 0.1693228108955401 chr3 198022430 2534494 0.012799024837741866 0.1188118351269205 chr4 191154276 3497585 0.01829718420737813 0.1506862048417804 chr5 180915260 2521032 0.013934877577491253 0.12370628953086339 chr6 171115067 1956373 0.01143308438175114 0.1264484922621797 chr7 159138663 2329992 0.014641269167882854 0.19935833550843973 chr8 146364022 5384963 0.03679157573300357 0.22048665356355798 chr9 141213431 1837225 0.01301027095645031 0.14480639674541423 chr10 135534747 2318277 0.017104669107472492 0.1735461887370124 chr11 135006516 1600344 0.011853827855242187 0.14369805837258423 chr12 133851895 2148048 0.016047946127322292 0.13369348315186982 chr13 115169878 1248892 0.010843911808259448 0.10866706177091126 chr14 107349540 1090099 0.01015466857147222 0.10714330341771464 chr15 102531392 1133576 0.011055892033534472 0.11076207282483583 chr16 90354753 1394590 0.01543460585853187 0.13632319506371723 chr17 81195210 1551566 0.01910908291264965 0.15004229420310924 chr18 78077248 1338374 0.017141664624244952 0.2502744024304406 chr19 59128983 927221 0.015681328393556168 0.2021775074266255 chr20 63025520 1320123 0.02094584860228047 0.1522543147477704 chr21 48129895 616080 0.012800360358151623 0.12683117893171073 chr22 51304566 387226 0.0075475933272683765 0.0908211265677193 chrMT 16571 2335 0.14090881660732604 0.37298002463710295 chrX 155270560 2758764 0.01776746345218308 0.14698828989246138 chrY 59373566 155055 0.00261151570380664 0.08369866153353525