Oryza sativa Japonica Group vs Oryza sativa Indica Group LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) 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

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
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
     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 Indica Group
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 127,294 alignment blocks

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

Uncovered: 64,351,985 out of 374,424,240
Covered: 310,072,255 out of 374,424,240

Uncovered: 270,394 out of 34,124,807
Matches: 33,318,603 out of 34,124,807
Mismatches: 446,546 out of 34,124,807
Insertions: 89,264 out of 34,124,807
Identity over aligned base-pairs: 98.4%

Oryza sativa Indica Group

Uncovered: 143,812,226 out of 427,004,890
Covered: 283,192,664 out of 427,004,890

Uncovered: 6,417,323 out of 45,465,969
Matches: 38,706,848 out of 45,465,969
Mismatches: 277,779 out of 45,465,969
Insertions: 64,019 out of 45,465,969
Identity over aligned base-pairs: 99.1%