In this section

Oryza sativa Japonica Group vs Triticum timopheevii LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Triticum timopheevii (Triticum timopheevii, WRC_timopheevii_genome_with_organelles) 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 timopheevii
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 589,190 alignment blocks

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

Uncovered: 291,247,255 out of 375,049,285
Covered: 83,802,030 out of 375,049,285

Uncovered: 3,374,912 out of 34,818,902
Matches: 24,411,042 out of 34,818,902
Mismatches: 6,141,610 out of 34,818,902
Insertions: 891,338 out of 34,818,902
Identity over aligned base-pairs: 77.6%

Triticum timopheevii

Uncovered: 9,081,348,250 out of 9,351,419,471
Covered: 270,071,221 out of 9,351,419,471

Uncovered: 78,435,427 out of 175,451,481
Matches: 72,747,261 out of 175,451,481
Mismatches: 21,670,946 out of 175,451,481
Insertions: 2,597,847 out of 175,451,481
Identity over aligned base-pairs: 75.0%

Block size distribution

Size range All 589,190 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,956
27.3 kb
10 bp - 100 bp
84,870
5.5 Mb
36,430
2.6 Mb
100 bp - 1 kb
413,023
155.0 Mb
191,377
69.0 Mb
1 kb - 10 kb
86,340
147.2 Mb
81,374
200.7 Mb
10 kb - 100 kb
1
13.5 kb
2,240
35.1 Mb
100 kb - 1 Mb
4
462.1 kb