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Oryza sativa Japonica Group vs Oryza sativa (Geng/Japonica-sbtrp var. Chao Meo) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Geng/Japonica-sbtrp var. Chao Meo) (Oryza sativa tropical japonica subgroup, Os132278RS1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 111. 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 GroupOryza sativa (Geng/Japonica-sbtrp var. Chao Meo)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 55,983 alignment blocks

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

Uncovered: 30,617,490 out of 375,049,285
Covered: 344,431,795 out of 375,049,285

Uncovered: 188,885 out of 34,818,902
Matches: 34,436,342 out of 34,818,902
Mismatches: 163,111 out of 34,818,902
Insertions: 30,564 out of 34,818,902
Identity over aligned base-pairs: 99.4%

Oryza sativa (Geng/Japonica-sbtrp var. Chao Meo)

Uncovered: 38,482,092 out of 383,243,376
Covered: 344,761,284 out of 383,243,376

Uncovered: 408,571 out of 42,807,831
Matches: 42,060,266 out of 42,807,831
Mismatches: 292,722 out of 42,807,831
Insertions: 46,272 out of 42,807,831
Identity over aligned base-pairs: 99.2%

Block size distribution

Size range All 55,983 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
699
4.1 kb
10 bp - 100 bp
11,400
661.0 kb
5,437
335.1 kb
100 bp - 1 kb
27,282
9.6 Mb
13,077
4.7 Mb
1 kb - 10 kb
10,767
37.2 Mb
3,896
9.0 Mb
10 kb - 100 kb
4,933
154.3 Mb
195
4.2 Mb
100 kb - 1 Mb
902
160.9 Mb
6
1.6 Mb
1 Mb - 10 Mb
1
4.5 Mb
10 Mb - 100 Mb
12
338.4 Mb