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Pythium iwayamai vs Giardia intestinalis - GCA_000002435.2 LastZ results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Pythium iwayamai 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

ParameterPythium iwayamaiGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,700 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium iwayamai

Uncovered: 42,604,282 out of 43,199,174
Covered: 594,892 out of 43,199,174

Uncovered: 19,038,857 out of 19,552,457
Matches: 305,043 out of 19,552,457
Mismatches: 187,694 out of 19,552,457
Insertions: 20,863 out of 19,552,457
Identity over aligned base-pairs: 59.4%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,683,505 out of 12,078,186
Covered: 394,681 out of 12,078,186

Uncovered: 9,084,100 out of 9,469,365
Matches: 224,046 out of 9,469,365
Mismatches: 141,939 out of 9,469,365
Insertions: 19,280 out of 9,469,365
Identity over aligned base-pairs: 58.2%

Block size distribution

Size range All 1,700 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
14.0 bp
10 bp - 100 bp
230
15.6 kb
94
6.9 kb
100 bp - 1 kb
1,332
482.4 kb
782
342.7 kb
1 kb - 10 kb
136
205.7 kb
170
343.3 kb
10 kb - 100 kb
1
10.7 kb