Is sample "GF_0169" a male or XO female? (lm 5/7/2012)
There is a "male-like" imbalance in the number of maternal reads vs. paternal reads.
There is a "female-like" reduction in reads to the Y chromosome.
What is wrong with samples "GH_0081(M)" and "GH_0087(F)"? Are they a mix of lanes from two animals? (lm 5/7/2012)
Mitochondria read ratios are inconsistent. Paternal counts are too high. In "GH_0081(M)" the paternal read counts are 37% greater than the maternal; such a skew is unlikely due to a reciprocal.
"GH_0081(M)" has too many paternal reads on X (should have none)
The number of reads mapping to Y in "GH_0087(F)" is atypical of (higher than) other GH samples.
Why are the paternal mitochondrial read so high for sample "FG_0122(M)"? (lm 5/8/2012)
What is wrong with inbred sample "FF_6136(F)"? (lm 5/9/2012)
Based on gene expression on chromosome X it appears more like an F1 (FG? or GF?)
Many Sanger high-confidence SNPs are inconsistent with our inbred alignments (lm 5/9/2012)
Examining inbreds at the annotated Sanger SNP positions shows evidence of multiple alleles. More than I would expect by noise alone
The inconsistent SNP positions appear to be cross specific (will add more explaination later).
Resolved Problems:
Why do the allelic ratios on X for the GH and HG samples stop at 100MB? (lm 5/7/2012) Fixed with latest bam files (lm 5/8/2012: there must have been a problem with the bamfiles that extracted only X).
Resources:
Spreadsheet identifying problem F1 samples (F1sanity.xls)