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Oryza sativa Indica Group vs Oryza brachyantha LastZ results

Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 67. Oryza sativa Indica 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 Indica GroupOryza brachyantha
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 284,996 alignment blocks

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

Uncovered: 289,008,263 out of 427,004,890
Covered: 137,996,627 out of 427,004,890

Uncovered: 8,260,664 out of 45,465,969
Matches: 31,694,338 out of 45,465,969
Mismatches: 4,707,305 out of 45,465,969
Insertions: 803,662 out of 45,465,969
Identity over aligned base-pairs: 85.2%

Oryza brachyantha

Uncovered: 153,542,668 out of 260,838,168
Covered: 107,295,500 out of 260,838,168

Uncovered: 4,534,293 out of 33,473,466
Matches: 25,623,489 out of 33,473,466
Mismatches: 2,881,197 out of 33,473,466
Insertions: 434,487 out of 33,473,466
Identity over aligned base-pairs: 88.5%

Block size distribution

Size range All 284,996 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,022
25.8 kb
10 bp - 100 bp
50,570
3.1 Mb
21,655
1.5 Mb
100 bp - 1 kb
191,044
68.5 Mb
67,463
20.3 Mb
1 kb - 10 kb
39,352
75.6 Mb
8,559
20.1 Mb
10 kb - 100 kb
8
86.9 kb
242
5.1 Mb
100 kb - 1 Mb
4
625.3 kb
1 Mb - 10 Mb
9
57.5 Mb
10 Mb - 100 Mb
3
42.2 Mb