In this section

Arabidopsis thaliana vs Oryza sativa Indica Group LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 90. Arabidopsis thaliana 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

ParameterArabidopsis thalianaOryza sativa Indica Group
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 119,378 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,204,588 out of 119,667,750
Covered: 26,463,162 out of 119,667,750

Uncovered: 14,250,221 out of 33,775,569
Matches: 12,685,684 out of 33,775,569
Mismatches: 6,450,770 out of 33,775,569
Insertions: 388,894 out of 33,775,569
Identity over aligned base-pairs: 65.0%

Oryza sativa Indica Group

Uncovered: 396,245,759 out of 427,004,890
Covered: 30,759,131 out of 427,004,890

Uncovered: 24,597,243 out of 45,465,969
Matches: 13,396,390 out of 45,465,969
Mismatches: 6,971,101 out of 45,465,969
Insertions: 501,235 out of 45,465,969
Identity over aligned base-pairs: 64.2%

Block size distribution

Size range All 119,378 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
957
4.9 kb
10 bp - 100 bp
18,591
1.3 Mb
3,423
246.6 kb
100 bp - 1 kb
92,988
30.9 Mb
24,931
10.4 Mb
1 kb - 10 kb
6,842
10.0 Mb
15,126
31.1 Mb
10 kb - 100 kb
35
420.0 kb