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Oryza sativa Japonica Group vs Triticum turgidum LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Triticum turgidum (Triticum turgidum subsp. durum, Svevo.v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. 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 turgidum
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 671,091 alignment blocks

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

Uncovered: 290,020,848 out of 375,049,285
Covered: 85,028,437 out of 375,049,285

Uncovered: 3,152,204 out of 34,424,450
Matches: 24,155,722 out of 34,424,450
Mismatches: 6,235,839 out of 34,424,450
Insertions: 880,685 out of 34,424,450
Identity over aligned base-pairs: 77.2%

Triticum turgidum

Uncovered: 10,182,497,900 out of 10,463,058,104
Covered: 280,560,204 out of 10,463,058,104

Uncovered: 8,310,617 out of 88,577,667
Matches: 61,802,295 out of 88,577,667
Mismatches: 16,600,913 out of 88,577,667
Insertions: 1,863,842 out of 88,577,667
Identity over aligned base-pairs: 77.0%

Block size distribution

Size range All 671,091 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,350
24.7 kb
10 bp - 100 bp
108,418
7.2 Mb
59,292
4.2 Mb
100 bp - 1 kb
475,493
172.9 Mb
245,355
84.2 Mb
1 kb - 10 kb
82,821
140.0 Mb
77,518
194.8 Mb
10 kb - 100 kb
9
110.8 kb
2,436
37.0 Mb
100 kb - 1 Mb
1
100.3 kb