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Arabidopsis thaliana vs Setaria viridis LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Setaria viridis (Setaria viridis, Setaria_viridis_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 thalianaSetaria viridis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 119,456 alignment blocks

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

Uncovered: 93,245,268 out of 119,667,750
Covered: 26,422,482 out of 119,667,750

Uncovered: 14,184,803 out of 33,775,569
Matches: 12,687,359 out of 33,775,569
Mismatches: 6,506,511 out of 33,775,569
Insertions: 396,896 out of 33,775,569
Identity over aligned base-pairs: 64.8%

Setaria viridis

Uncovered: 364,843,522 out of 395,731,502
Covered: 30,887,980 out of 395,731,502

Uncovered: 20,656,993 out of 41,880,594
Matches: 13,602,114 out of 41,880,594
Mismatches: 7,117,278 out of 41,880,594
Insertions: 504,209 out of 41,880,594
Identity over aligned base-pairs: 64.1%

Block size distribution

Size range All 119,456 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,025
5.2 kb
10 bp - 100 bp
18,584
1.3 Mb
3,313
234.4 kb
100 bp - 1 kb
93,005
30.8 Mb
24,254
10.3 Mb
1 kb - 10 kb
6,842
10.0 Mb
15,277
31.1 Mb
10 kb - 100 kb
36
438.1 kb