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. 2020 Feb 19;117(8):3910–3912. doi: 10.1073/pnas.1920788117

Table 1.

Mutations detected within the coding sequence for glpK between 200 longitudinal and 62 replicate isolate pairs

H37Rv reference position H37Rv reference allele Alternate allele Change in allele frequency H37Rv locus tag Isolate pair type Gene position Variant type Amino acid change/indel type Alternate allele frequency A Alternate allele frequency B
4138945 A G 0.41 Rv3696c Longitudinal 811 nSNP C271R 0.41 0
4138645 G A 0.93 Rv3696c Longitudinal 1111 nSNP P371S 0.93 0
4138599 C A 0.43 Rv3696c Longitudinal 1157 nSNP R386L 0.43 0
4138398 G A 0.79 Rv3696c Longitudinal 1358 nSNP A453V 0.79 0
4139183 A AC 0.386781609 Rv3696c Longitudinal 573 Indel Insertion 0.903448276 0.516666667
4139183 A AC 0.573228751 Rv3696c Longitudinal 573 Indel Insertion 0.910891089 0.337662338
4139183 A AC 0.941666667 Rv3696c Longitudinal 573 Indel Insertion 0 0.941666667
4139183 A AC 0.633663366 Rv3696c Longitudinal 573 Indel Insertion 0 0.633663366
4139183 A AC 0.894736842 Rv3696c Longitudinal 573 Indel Insertion 0.894736842 0
4139183 A AC 0.882352941 Rv3696c Longitudinal 573 Indel Insertion 0 0.882352941
4139183 A AC 0.534482759 Rv3696c Longitudinal 573 Indel Insertion 0 0.534482759
4139183 A AC 0.95323741 Rv3696c Longitudinal 573 Indel Insertion 0 0.95323741
4139183 A AC 0.326530612 Rv3696c Longitudinal 573 Indel Insertion 0.326530612 0
4139183 A AC 0.827160494 Rv3696c Longitudinal 573 Indel Insertion 0 0.827160494
4139183 A AC 0.818181818 Rv3696c Longitudinal 573 Indel Insertion 0 0.818181818
4139183 A AC 0.873417722 Rv3696c Longitudinal 573 Indel Insertion 0 0.873417722
4139183 A AC 0.627118644 Rv3696c Longitudinal 573 Indel Insertion 0 0.627118644
4139183 AC A 0.495798319 Rv3696c Longitudinal 573 Indel Deletion 0 0.495798319
4138684 CG C 0.343065693 Rv3696c Longitudinal 1072 Indel Deletion 0.343065693 0
4138376 C CA 0.507246377 Rv3696c Longitudinal 1380 Indel Insertion 0 0.507246377
4139424 G A 0.28 Rv3696c Replicate 332 nSNP A111V 0 0.28
4139083 G A 0.38 Rv3696c Replicate 673 nSNP R225W 0 0.38
4138995 G A 0.29 Rv3696c Replicate 761 nSNP P254L 0 0.29
4138398 G A 0.81 Rv3696c Replicate 1358 nSNP A453V 0.02 0.83
4138326 A G 0.47 Rv3696c Replicate 1430 nSNP L477P 0 0.47
4139183 A AC 0.521403509 Rv3696c Replicate 573 Indel Insertion 0.894736842 0.373333333
4139183 A AC 0.470588235 Rv3696c Replicate 573 Indel Insertion 0.5 0.970588235
4139183 A AC 0.85 Rv3696c Replicate 573 Indel Insertion 0.85 0
4139183 A AC 0.25 Rv3696c Replicate 573 Indel Insertion 0.25 0
4139183 A AC 0.447058824 Rv3696c Replicate 573 Indel Insertion 0.447058824 0
4139183 A AC 0.670807453 Rv3696c Replicate 573 Indel Insertion 0.670807453 0
4139183 AC A 0.237288136 Rv3696c Replicate 573 Indel Deletion 0.237288136 0
4139183 A AC 0.534482759 Rv3696c Replicate 573 Indel Insertion 0.534482759 0
4139183 A AC 0.513513514 Rv3696c Replicate 573 Indel Insertion 0.513513514 0
4139183 A AC 0.573863636 Rv3696c Replicate 573 Indel Insertion 0.573863636 0
4139183 A AC 0.561643836 Rv3696c Replicate 573 Indel Insertion 0.561643836 0
4139183 A AC 0.348314607 Rv3696c Replicate 573 Indel Insertion 0.348314607 0
4139183 A AC 0.868686869 Rv3696c Replicate 573 Indel Insertion 0.868686869 0

SNPs were reported for a pair only if the alternate allele frequency between both isolates changed by at least 25%. Indels were reported if the alternate allele was detected at any allele frequency in at least one isolate for each pair. In a majority of cases, the mutant allele was detectable only in one of the isolates in each pair. The values in columns alternate allele frequency A and alternate allele frequency B are ordered according to sample collection dates for the longitudinal pairs. This ordering is arbitrary for replicate pairs since we did not have sample collection dates for the replicate isolates.