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Triticum aestivum vs Oryza sativa Japonica Group LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. Triticum aestivum was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterTriticum aestivumOryza sativa Japonica Group
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 1,354,149 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 13,961,074,617 out of 14,547,261,565
Covered: 586,186,948 out of 14,547,261,565

Uncovered: 12,047,551 out of 136,655,258
Matches: 96,121,876 out of 136,655,258
Mismatches: 25,678,140 out of 136,655,258
Insertions: 2,807,691 out of 136,655,258
Identity over aligned base-pairs: 77.1%

Oryza sativa Japonica Group

Uncovered: 278,641,612 out of 375,049,285
Covered: 96,407,673 out of 375,049,285

Uncovered: 2,740,097 out of 34,403,043
Matches: 24,383,725 out of 34,403,043
Mismatches: 6,365,365 out of 34,403,043
Insertions: 913,856 out of 34,403,043
Identity over aligned base-pairs: 77.0%

Block size distribution

Size range All 1,354,149 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7,246
39.6 kb
10 bp - 100 bp
235,789
15.4 Mb
148,502
10.0 Mb
100 bp - 1 kb
937,698
332.0 Mb
525,909
175.7 Mb
1 kb - 10 kb
173,404
301.4 Mb
170,647
404.1 Mb
10 kb - 100 kb
12
146.2 kb
3,821
58.7 Mb
100 kb - 1 Mb
4
439.2 kb