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Ashbya gossypii vs Puccinia triticina LastZ results

Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) and Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Ashbya gossypii 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

ParameterAshbya gossypiiPuccinia triticina
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,532 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Ashbya gossypii

Uncovered: 8,646,335 out of 9,119,312
Covered: 472,977 out of 9,119,312

Uncovered: 6,549,034 out of 7,019,450
Matches: 289,163 out of 7,019,450
Mismatches: 170,950 out of 7,019,450
Insertions: 10,303 out of 7,019,450
Identity over aligned base-pairs: 61.5%

Puccinia triticina

Uncovered: 162,281,937 out of 162,948,716
Covered: 666,779 out of 162,948,716

Uncovered: 13,441,958 out of 13,973,123
Matches: 324,767 out of 13,973,123
Mismatches: 183,295 out of 13,973,123
Insertions: 23,103 out of 13,973,123
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 2,532 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
19.0 bp
10 bp - 100 bp
492
35.6 kb
64
4.8 kb
100 bp - 1 kb
1,972
579.2 kb
683
303.1 kb
1 kb - 10 kb
63
93.0 kb
229
399.9 kb