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Oryza sativa Japonica Group vs Triticum urartu LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Triticum urartu (Triticum urartu, IGDB) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. 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 urartu
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 260,609 alignment blocks

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

Uncovered: 300,371,389 out of 375,049,285
Covered: 74,677,896 out of 375,049,285

Uncovered: 4,444,899 out of 34,424,450
Matches: 23,116,851 out of 34,424,450
Mismatches: 6,019,022 out of 34,424,450
Insertions: 843,678 out of 34,424,450
Identity over aligned base-pairs: 77.1%

Triticum urartu

Uncovered: 4,743,243,418 out of 4,851,895,022
Covered: 108,651,604 out of 4,851,895,022

Uncovered: 7,487,603 out of 41,813,638
Matches: 26,733,691 out of 41,813,638
Mismatches: 6,874,746 out of 41,813,638
Insertions: 717,598 out of 41,813,638
Identity over aligned base-pairs: 77.9%

Block size distribution

Size range All 260,609 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,168
12.3 kb
10 bp - 100 bp
37,055
2.4 Mb
14,596
1.0 Mb
100 bp - 1 kb
183,999
70.2 Mb
76,714
28.0 Mb
1 kb - 10 kb
37,381
63.4 Mb
33,800
89.3 Mb
10 kb - 100 kb
6
91.6 kb
1,200
17.7 Mb