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Oryza sativa Japonica Group vs Triticum spelta LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Triticum spelta (Triticum spelta, PGSBv2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 113. Oryza sativa Japonica Group 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

ParameterOryza sativa Japonica GroupTriticum spelta
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 827,238 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 288,190,485 out of 375,049,285
Covered: 86,858,800 out of 375,049,285

Uncovered: 3,265,856 out of 34,818,902
Matches: 24,439,193 out of 34,818,902
Mismatches: 6,208,394 out of 34,818,902
Insertions: 905,459 out of 34,818,902
Identity over aligned base-pairs: 77.5%

Triticum spelta

Uncovered: 13,608,932,377 out of 14,000,336,401
Covered: 391,404,024 out of 14,000,336,401

Uncovered: 17,891,159 out of 128,797,843
Matches: 85,813,534 out of 128,797,843
Mismatches: 22,607,473 out of 128,797,843
Insertions: 2,485,677 out of 128,797,843
Identity over aligned base-pairs: 77.4%

Block size distribution

Size range All 827,238 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6,735
36.9 kb
10 bp - 100 bp
118,555
7.7 Mb
51,618
3.7 Mb
100 bp - 1 kb
578,220
218.0 Mb
264,502
95.1 Mb
1 kb - 10 kb
123,722
212.5 Mb
114,432
287.8 Mb
10 kb - 100 kb
6
71.7 kb
3,318
51.2 Mb
100 kb - 1 Mb
4
443.4 kb