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Ashbya gossypii vs Trichoderma virens LastZ results

Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) 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 gossypiiTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,352 alignment blocks

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

Uncovered: 8,246,780 out of 9,119,312
Covered: 872,532 out of 9,119,312

Uncovered: 6,151,886 out of 7,019,450
Matches: 530,511 out of 7,019,450
Mismatches: 309,759 out of 7,019,450
Insertions: 27,294 out of 7,019,450
Identity over aligned base-pairs: 61.1%

Trichoderma virens

Uncovered: 37,929,258 out of 39,022,666
Covered: 1,093,408 out of 39,022,666

Uncovered: 16,483,213 out of 17,541,951
Matches: 638,030 out of 17,541,951
Mismatches: 377,012 out of 17,541,951
Insertions: 43,696 out of 17,541,951
Identity over aligned base-pairs: 60.3%

Block size distribution

Size range All 2,352 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
15.0 bp
10 bp - 100 bp
287
19.9 kb
53
3.9 kb
100 bp - 1 kb
1,767
695.9 kb
763
416.2 kb
1 kb - 10 kb
295
455.7 kb
433
751.4 kb