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Oryza sativa Japonica Group vs Avena sativa Sang LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Avena sativa Sang (Avena sativa, Asativa_sang.v1.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 109. 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 GroupAvena sativa Sang
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 676,385 alignment blocks

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

Uncovered: 285,542,633 out of 375,049,285
Covered: 89,506,652 out of 375,049,285

Uncovered: 3,325,503 out of 34,424,450
Matches: 23,643,814 out of 34,424,450
Mismatches: 6,578,684 out of 34,424,450
Insertions: 876,449 out of 34,424,450
Identity over aligned base-pairs: 76.0%

Avena sativa Sang

Uncovered: 10,694,200,589 out of 11,012,379,496
Covered: 318,178,907 out of 11,012,379,496

Uncovered: 13,162,957 out of 103,635,760
Matches: 70,682,502 out of 103,635,760
Mismatches: 17,889,066 out of 103,635,760
Insertions: 1,901,235 out of 103,635,760
Identity over aligned base-pairs: 78.1%

Block size distribution

Size range All 676,385 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,823
32.0 kb
10 bp - 100 bp
96,259
6.2 Mb
39,864
2.8 Mb
100 bp - 1 kb
471,594
180.8 Mb
202,880
73.9 Mb
1 kb - 10 kb
102,706
175.7 Mb
83,864
205.2 Mb
10 kb - 100 kb
3
32.4 kb
2,916
56.4 Mb
100 kb - 1 Mb
61
12.9 Mb
1 Mb - 10 Mb
7
11.5 Mb