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Arabidopsis thaliana vs Nymphaea colorata LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Nymphaea colorata (Nymphaea colorata, ASM883128v1) 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 thalianaNymphaea colorata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 124,664 alignment blocks

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

Uncovered: 92,800,036 out of 119,667,750
Covered: 26,867,714 out of 119,667,750

Uncovered: 13,227,019 out of 33,775,569
Matches: 13,484,707 out of 33,775,569
Mismatches: 6,649,126 out of 33,775,569
Insertions: 414,717 out of 33,775,569
Identity over aligned base-pairs: 65.6%

Nymphaea colorata

Uncovered: 379,671,897 out of 408,396,728
Covered: 28,724,831 out of 408,396,728

Uncovered: 14,970,404 out of 32,910,518
Matches: 11,613,093 out of 32,910,518
Mismatches: 5,855,253 out of 32,910,518
Insertions: 471,768 out of 32,910,518
Identity over aligned base-pairs: 64.7%

Block size distribution

Size range All 124,664 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
929
4.6 kb
10 bp - 100 bp
20,070
1.4 Mb
5,163
368.9 kb
100 bp - 1 kb
97,928
30.6 Mb
29,820
11.7 Mb
1 kb - 10 kb
5,737
8.3 Mb
14,211
28.0 Mb
10 kb - 100 kb
22
285.9 kb