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Oryza sativa Japonica Group vs Oryza glaberrima LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 73. 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)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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 GroupOryza glaberrima
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 183,406 alignment blocks

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

Uncovered: 104,728,015 out of 375,049,285
Covered: 270,321,270 out of 375,049,285

Uncovered: 1,693,008 out of 34,818,902
Matches: 31,639,376 out of 34,818,902
Mismatches: 1,277,289 out of 34,818,902
Insertions: 209,229 out of 34,818,902
Identity over aligned base-pairs: 95.5%

Oryza glaberrima

Uncovered: 88,192,351 out of 316,419,574
Covered: 228,227,223 out of 316,419,574

Uncovered: 4,001,728 out of 36,293,721
Matches: 31,970,666 out of 36,293,721
Mismatches: 268,415 out of 36,293,721
Insertions: 52,912 out of 36,293,721
Identity over aligned base-pairs: 99.0%

Block size distribution

Size range All 183,406 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,860
10.5 kb
10 bp - 100 bp
37,456
2.2 Mb
20,621
1.3 Mb
100 bp - 1 kb
97,132
34.7 Mb
48,338
16.9 Mb
1 kb - 10 kb
40,883
134.9 Mb
12,685
29.6 Mb
10 kb - 100 kb
6,075
102.1 Mb
219
4.5 Mb
100 kb - 1 Mb
11
2.2 Mb
10 Mb - 100 Mb
12
219.6 Mb