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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.
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Genome Biology

ISSN: 1474-760X

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