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Arabidopsis thaliana vs Capsicum annuum LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Capsicum annuum (Capsicum annuum, ASM51225v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. 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 thalianaCapsicum annuum
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 197,496 alignment blocks

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

Uncovered: 86,333,345 out of 119,667,750
Covered: 33,334,405 out of 119,667,750

Uncovered: 9,625,824 out of 33,775,569
Matches: 16,026,272 out of 33,775,569
Mismatches: 7,585,171 out of 33,775,569
Insertions: 538,302 out of 33,775,569
Identity over aligned base-pairs: 66.4%

Capsicum annuum

Uncovered: 3,010,943,505 out of 3,063,864,880
Covered: 52,921,375 out of 3,063,864,880

Uncovered: 14,072,818 out of 39,113,865
Matches: 16,708,122 out of 39,113,865
Mismatches: 7,730,009 out of 39,113,865
Insertions: 602,916 out of 39,113,865
Identity over aligned base-pairs: 66.7%

Block size distribution

Size range All 197,496 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,304
6.9 kb
10 bp - 100 bp
32,354
2.2 Mb
11,320
808.5 kb
100 bp - 1 kb
153,261
48.7 Mb
60,064
21.8 Mb
1 kb - 10 kb
10,569
16.1 Mb
20,933
43.4 Mb
10 kb - 100 kb
8
112.6 kb
87
1.2 Mb