Interpreting trioeval results

[sheinasim]

Hello there!

I am trying to evaluate my results using trioeval to determine which combination of parents is the correct one for two offspring that were sequenced, and I was wondering what are reasonable/appropriate switch, hamming, and error rates I should expect if I used the correct parents?

I ran trio eval for both haplotypes of two individuals using different combinations of crosses, and there are the results of the error values and assembly sizes (reformatted for easier viewing):

Individual Cross Haplotype Assembly size SwitchErr HammingErr Error rate Female3_A5XT3_1 MomGSS_DadWT hap1 416.286 MB 0.009677 0.029152 0.192823 Female3_A5XT3_1 MomGSS_DadWT hap2 455.511 MB 0.030446 0.221999 0.261755 Female3_A5XT3_1 MomWT_DadGSS hap1 139.717 MB 0.031343 0.143641 0.205221 Female3_A5XT3_1 MomWT_DadGSS hap2 516.164 MB 0.004239 0.005917 0.206673 Female4_T3XA5_8 MomGSS_DadWT hap1 317.587 MB 0.049077 0.285274 0.334955 Female4_T3XA5_8 MomGSS_DadWT hap2 495.368 MB 0.006831 0.027895 0.028415 Female4_T3XA5_8 MomWT_DadGSS hap1 163.095 MB 0.058849 0.117145 0.142917 Female4_T3XA5_8 MomWT_DadGSS hap2 491.974 MB 0.027789 0.123784 0.142537

Based on these assembly sizes and error values, is it possible to determine which combination of parents (cross) is the correct one for each of the Individuals (Female 3 and Female 4)? They should have opposite parents (not the same cross).

Thanks for your help, and please let me know if my question requires clarification!

Best wishes, Sheina

[chhylp123]

I don't know. For non-plant genomes, I guess the hamming error rate should be smaller than 1%. For plant genomes, the hamming error rate might be a little bit higher, so 3% might be acceptable. The main problem is the last column. For all assemblies except hap2 of Female4_T3XA5_8 MomGSS_DadWT, the error rate is too high.