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. 2014 Dec 17;199(2):555–571. doi: 10.1534/genetics.114.171124

Table 1. Mutations identified in the CBM lines.

CUP1 Genome position Mutation Position Amino acid
CBM line coverage (chr.bp) Gene (Watson strand) (from 5′ end) change Exchangeability
CBM1 1.61 X.412600 VTC4 C > T 800 Trp > Stop
XI.105507 FAS1 G > T 4837 Val > Phe 0.207
XVI.420661 Intergenic A > T
CBM2 2.00 ChrII aneuploidy
CBM3 2.48 VII.150650 Intergenic G > T
ChrII aneuploidy
CBM4 3.26 mito.24277a COX1b 1D indel (GG C/- CC) 10460 Intron
CBM5 3.78 X.413174 VTC4 C > A 226 Glu > Stop
X.654261 Intergenicc T > C
XIV.284255 Intergenic T > G
CBM6 3.69 III.100061 BUD3 G > A 3781 Gly > Arg 0.178
IV.319466 VAM6 T > A 655 Lys > Stop
mito.59168 21S_RRNA A > G 1160 Lys > Arg 0.440
mito.69322 tRNA-Arg C > G 34 Arg > Gly 0.251
CBM7 0.91 II.365359 TRM7 C > T 361 Val > Ile 0.537
III.306327 Intergenic G > T
IV.143017 YDL176W G > T 921 Ser > Ser
IV.177435 CLB3 T > G 663 Thr > Thr
V.392908 BOI2 C > T 805 Glu > Lys 0.323
VII.949946 SMI1 C > A 954 Lys > Asn 0.457
IX.370383 Intergenic C > G
XV.215888 MAM3 C > G 250 Gly > Arg 0.178
ChrVIII aneuploidy
ChrXVI aneuploidy
CBM11 2.46 X.413020 VTC4 1D indel (GG A/- AA) 380 Phe > Ser+frameshift
XI.566200 CCP1 A > G 999 Phe > Phe
XII.605283 Intergenic 1D indel (TT A/- AA)
ChrII aneuploidy
CBM13 4.02 X.412247 VTC4 C > A 1153 Glu > Stop
X.654261 Intergenicc T > C
CBM14 2.15 XV.215018 MAM3 C > T 1120 Val > Ile 0.537
CBM16 0.28 VII.480836 PMA1 A > T 1831 Phe > Ile 0.181
ChrII aneuploidy
CBM17 0.98 X.412325 VTC4 A > G 1075 Tyr > His 0.197
XIII.711207 ESC1 C > T 4075 Leu > Phe 0.336
XIII.821262 FCP1 T > C 1007 Leu > Ser 0.212
ChrVIII aneuploidy
ChrXVI aneuploidy
CBM18 2.80 V.303094 VTC1 G > T 289 Asp > Tyr 0.227
VII.548326 GSC2 C > T 63 Asp > Asp
XI.646464-onwards FLO10d
CBM20 1.82 VII.480463 PMA1e G > T 2204 Ala > Asp 0.193
XV.215332 MAM3 C > T 806 Ser > Asn 0.390
XVI.84024 YPL247C C > T 173 Gly > Asp 0.188
ChrII aneuploidy
CBM21 1.12 VII.971165 PFK1 G > C 2570 Pro > Arg 0.254
X.654261 Intergenicc T > C
ChrII aneuploidy
ChrIII aneuploidy
ChrVIII aneuploidy
CBM22 0.78 V.302818 VTC1 1D indel (CA C/- CA) 13 Pro > His+frameshift
ChrVIII aneuploidy
ChrXVI aneuploidy
CBM24 0.77 IV.805485 Intergenic A > G
IV.805517 Intergenic G > A
CBM25 2.28 IV.527743-onwards ENA5f
XI.621992 MLP1 G > T 2188 Glu > Stop
CBM26 0.66 VII.480470 PMA1 T > G 2197 Thr > Pro 0.164
ChrI aneuploidy
ChrV aneuploidy
ChrVIII aneuploidy
CBM29 1.08 VII.1376 Intergenic A > C
VII.480463 PMA1e G > T 2204 Ala > Asp 0.193
XV.566240 Intergenic G > C
ChrII aneuploidy
CBM30 3.30 ChrII aneuploidy
CBM33 2.40 VII.618173 VHT1 G > C 1686 Ile > Met 0.279
VIII.321332 SBE22 A > T 919 Met > Leu 0.513
X.412080 VTC4g C > T 1320 Trp > Stop
mito.24277a COX1b 1D indel (GG C/- CC) 10460 Intron
CBM34 2.92 X.412080 VTC4g C > T 1320 Trp > Stop
XI.364518 Intergenic Complex 1I indel (GA > AAT)
mito.24277a COX1b 1D indel (GG C/- CC) 10460 Intron
CBM36 2.15 X.412080 VTC4g C > T 1320 Trp > Stop
mito.24277a COX1b 1D indel (GG C/- CC) 10460 Intron
CBM37 2.04 X.412080 VTC4g C > T 1320 Trp > Stop
mito.24277a COX1b 1D indel (GG C/- CC) 10460 Intron
CBM44h 1.39 X.412080 VTC4g C > T 1320 Trp > Stop
mito.24277a COX1b 1D indel (GG C/- CC) 10460 Intron
CBM45 2.68 X.412080 VTC4g C > T 1320 Trp > Stop
mito.24277a COX1b 1D indel (GG C/- CC) 10460 intron
CBM46 2.75 X.412643 VTC4 T > A 757 Arg > Stop
XI.438478 DID4 A > G 701 Gln > Arg 0.366
CBM47 2.34 V.302909 VTC1 C > A 104 Ser > Stop
CBM49 3.14 V.438349 Intergenic G > C
XII.1034221 HMG2 C > T 1595 Pro > Leu 0.258
XIII.420239 Intergenic A > C
XIV.265933 GCR2 T > A 598 Lys > Stop
CBM51 2.50 II.444465 FES1 C > T 229 Asp > Asn 0.201
IV.310552 Intergenic A > G
CBM53 2.88 V.180433 PRP22 C > T 1593 Ile > Ile
CBM54 1.98 VII.1077964 MAL12 G > T 1366 Gly > Stop
CBM55 2.25 (no mutations except to CUP1)

CUP1 coverage for each line is provided in the second column and does not account for additional copies via chrVIII aneuploidy.

a

This mutation falls in an intron of COX1 but causes a frameshift in an overlapping predicted gene, A15_Beta.

b

Identical COX1 mutation observed in seven different lines.

c

Identical intergenic mutation observed in three different lines.

d

The alignment formed a 100% match to the beginning of FLO10 until XI.647464, at which point the alignment switched to a perfect match to a similar region downstream, starting at XI.648031. In silico qPCR confirmed the absence of unique intervening sites (CACCAGCTCTTCCTGGTCGT and CACCAGCTCTTCCTGGTCGT) within the FASTQ files for CBM18 (but present in other CBM lines), indicating a deletion in this region.

e

Identical PMA1 mutation observed in two different lines.

f

The alignment within this region exhibited a 100% match to the beginning of ENA5 but switched to a 100% match to ENA1 from approximately site IV.527743, suggesting a deletion. Because of the highly repetitive nature of this array, in silico qPCR was unable to uniquely identify the missing positions.

g

Identical VTC4 mutation observed in six different lines.

h

CBM44 was sequenced from the original population, not the representative colony.