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Table 3 Details of the 23 SNVs analyzed further after filtering of exome sequence data

From: Exome sequencing identifies a missense mutation in Isl1associated with low penetrance otitis media in dearisch mice

         Dearisch    C3HeB/FeJ      
Gene name Location Predicted DNA change Reference (C57BL/6J) Consensus Genotype Consensus quality SNP quality Mapping quality Read depth Consensus Genotype Consensus quality SNP quality Mapping quality Read depth Cap seq C3H Cap seq Drsh Comments
1700001K19Rik 12:111907080 Nonsynonymous: H:L T A Hom 20 51 58 63 T/A Het 72 134 55 73 Deletion Deletion Misalignment around deletion.
1700104B16Rik 8:34841236 Nonsynonymous: H:D G G/C Het 76 76 55 54 G Hom 9 0 52 58 G/C G/C The dearisch read is correct; the incorrect C3H read has a very low consensus score
Acsl3 1:78692680 Stop gained C A Hom 7 25 49 16 A/C Het 9 9 56 15 C C Deep sequencing miscalled an A in Drsh and a C/A het in C3H. Neither of them have high consensus or SNP quality scores
Bcl2l14 6:134377474 Nonsynonymous: N:K T G Hom 3 36 50 64 G/A Het 9 10 60 61 NA Deletion Misalignment around deletion; low quality consensus and SNP scores
Btnl7 17:34670007 Nonsynonymous: G:R C C/T Het 6 96 48 30 T Hom 96 141 53 44 C/T C/T The C3H read has been miscalled as a homozygote
Catsper2 2:121223476 Nonsynonymous: N:D T C Hom 33 33 47 83 T/C Het 15 28 44 86 Deletion Deletion Misalignment around deletion
Col6a3 1:92672331 Essential splice site C G Hom 30 30 60 16 A Hom 33 33 29 18 NA Deletion Misalignment around deletion
Creb3l2 6:37284584 Essential splice site T C/T Het 38 38 54 23 T Hom 11 0 56 18 T T The dearisch read has been miscalled as a heterozygote
Gm10859 2:5833494 Nonsynonymous: I:V A A/G Het 41 48 56 18 A Hom 39 0 41 17 Deletion Deletion Misalignment around deletion
Gm11149 9:49380322 Nonsynonymous: Q:P A C Hom 0 36 54 30 G/C Het 0 23 52 30 Deletion Deletion Misalignment around deletion and low quality consensus scores
Gtf3c2 5:31476808 Nonsynonymous: E:G T C/T Het 25 25 49 39 T Hom 33 0 52 30 T T The dearisch read has been miscalled as a heterozygote. Its consensus and SNP quality scores are low
H2-Oa 17:34229420 Nonsynonymous: V:A T C/T Het 3 35 48 86 T Hom 39 0 46 79 Deletion Deletion Misalignment around deletion
Ido1 8:25703857 Nonsynonymous: R:K C C/T Het 21 21 50 30 C Hom 13 0 53 39 C C The dearisch read has been miscalled as a heterozygote. Its consensus and SNP quality scores are low
Isl1 13:117098488 Nonsynonymous: Y:C T C/T Het 199 228 60 66 T Hom 223 0 60 65 T C/T Confirmed by capillary sequencing
Mdc1 17:35984844 Nonsynonymous: E:D G T Hom 13 39 50 11 G/T Het 21 21 55 11 G G Deep sequencing miscalled a G as a T in Drsh and a G/T het in C3H. Neither of them has a very high consensus quality score
Olfr424 1:176066876 Essential splice site A G/T Het 4 58 58 88 T Hom 6 60 60 88 Insertion A Misalignment around insertion, also low consensus quality scores
Olfr573-ps1 7:110091057 Nonsynonymous: H:Q G T Hom 21 25 56 82 G/T Het 33 34 56 96 Deletion Deletion Misalignment around deletion
Olfr573-ps1 7:110091058 Nonsynonymous: H:L T A Hom 22 45 53 79 T/A Het 8 62 57 96 Deletion Deletion Misalignment around deletion
Olfr749 14:51356853 Nonsynonymous: Q:K G G/T Het 36 36 46 81 G Hom 17 0 39 62 Deletion Deletion Misalignment around deletion
Rsf1 7:104809403 Nonsynonymous: E:Q G G/C Het 17 22 54 47 G Hom 42 0 55 45 Deletion Deletion Misalignment around deletion
Rsf1 7:104809404 Nonsynonymous: E:V A A/T Het 14 22 54 47 A Hom 42 0 55 45 Deletion Deletion Misalignment around deletion
Sap30 bp 11:115825338 Nonsynonymous: A:T G A/G Het 31 31 55 61 G Hom 40 0 55 52 G G The dearisch read has been miscalled as a heterozygote
U1 1:172958261 Essential splice site T A/T Het 18 105 51 69 A Hom 26 75 51 58 Deletion Deletion Misalignment around deletion
  1. Capillary sequence results for the C3HeB/FeJ and dearisch DNA samples and comments on the reason for each false call are shown in the rightmost three columns. Fourteen of the calls were due to insertions or deletions present at that location that were identical in the two DNA samples, and the original call was due to different nucleotides affected by the deletion being called in the two samples. Het, heterozygous; Hom, homozygous; NA, sequence not available. Only one SNV was confirmed to be present in dearisch and not in C3HeB/FeJ or the C57BL/6J reference sequence, that in Isl1.