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Table 3 Determining which of the Env-encoding proviruses are likely to contribute to protein expression in the JVM2 cell line

From: Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines

Provirus

Number of uniquely mapping short reads (long reads in parentheses)a

Unique

env SNP allelesb

Number of short reads with unique SNP allele (long reads in parentheses)c

6q14.1

31 (0)

T(655)C

0 (0)

G(799)A

15 (0)

G(806)A

9 (0)

7p22.1a + bd

83 (0)

C(51)T

2 (0)

T(371)C

0 (0)

A(1116)G

0 (0)

8p23.1a

280 (1)

C(293)T

0 (0)e

G(958)A

365 (3)

G(1707)C

47 (0)

C(1983)T

1 (10)

11q22.1

33 (0)

C(537)

3 (0)f

G(1804)A

0 (2)f

G(2005)A

68 (3)f

12q14.1

962 (9)

G(96)A

275 (14)

T(465)C

12 (0)

C(586)A

89 (0)g

C(1484)T

75 (0)

19p12b

17 (1)

C(421)T

0 (0)h

C(970)G

0 (0)

C(1885)A

0 (1)i

A(1996)C

0 (0)

19q11

19 (1)

A(657)T

0 (1)

T(1355)C

0 (1)

T(1416)A

0 (0)

T(1416)A

0 (0)f

Xq21.33

52 (0)

C(52)A

0 (0)

G(827)A

16 (9)

G(1219)A

0 (1)

  1. aAll multi-mapping short reads excluded. All long reads have a mapping quality score of at least 20 (equivalent to a mapping error of p = 0.01)
  2. bEnv SNPs with allele that is found only in a single provirus. Positions relate to the Env alignment available in Additional file 9 with ancestral state inferred by commonality. In a few instances there is a second SNP within the 31 nt sequence and it is the combination that is unique
  3. cAverage number of short-read matches to a 31 nt sequence spanning the SNP that are unique to the provirus, with corresponding result from the single minION run (17 nt match) in parenthesis
  4. dBecause these proviruses are almost identical (resulting from a recent tandem duplication), and hence each would have few uniquely mapping reads, we repeated the analysis with provirus 7p22.1a deleted
  5. eSNP allele also present in unexpressed provirus Xq11.1
  6. fSNP allele also present in several other proviruses
  7. gSNP allele also in provirus 5p12, which has only 5 unique short-read hits
  8. hSNP allele also in unexpressed provirus 1q24.1
  9. iSNP allele also in the expressed provirus 6p21.1
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Mobile DNA

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