Haplogroup Quality score >1？

[nanshanjin]

The table is result of my haplogrep2 Quality score and some quality score >1 ，Is this situation right？

Rank	Quality	Not_Found_Polys
1	0.8112	16217C
1	0.8674	827G 5093C 6302G 9329A 10398G 12654G 13269G 15535T 16129A 16180d 16181d 16360T
1	0.9935	514d 515d 827G 5093C 6302G 9329A 10398G 12654G 13269G 15535T 16129A 16183C 16360T 16519C
1	0.912	310.1C 827G 5093C 6302G 9329A 10398G 12654G 13269G 15535T 16129A 16360T
1	0.8964	827G 5093C 6302G 9329A 10398G 12654G 13269G 15535T 16129A 16360T
1	1.1261	827G 5093C 9329A 10398G 13269G 15535T 16129A 16180d 16181d
1	0.9181	827G 5093C 6302G 9329A 12654G 13269G 15535T 16129A 16360T 16519C
1	0.9626	827G 6302G 9329A 10398G 12654G 15535T 16180d 16181d 16261T 16360T
1	1.035	514d 515d 827G 5093C 6302G 9329A 10398G 12654G 13269G 15535T 16129A 16360T 16519C
1	1.1058	827G 6302G 9329A 10398G 12654G 15535T 16183C 16360T 16519C

[stephenturner]

FWIW, I've seen this a couple of times as well, running the CLI version.

[seppinho]

any chances that you can share the file?
thanks!

[seppinho]

Would be fantastic if you can give the latest version a try. For FASTA, we excluded heteroplasmis sites from the input profile (resulted in score > 1) and adapted the range.

[stephenturner]

Thanks Sebastian! We were using a VCF file at the time. Unfortunately it's a sample that can't leave the building, but I'll see if we can test 2.2.6 on that sample.

[seppinho]

Thanks for the feedback, fyi the new version only fixes the FASTA related issues with the score. I'll look into the VCF problem, Hansi pointed out that this is related to insertions.