Table 1 Status of Genes Previously Reported as Affected by H37Ra-specific Mutations

(a) Genes with all High-Confidence Variants Contradicted by our Assembly

Rv0037c

Rv0037c

Probable conserved integral membrane protein

Rv0124

PE_PGRS2

PE-PGRS family protein PE_PGRS2

Rv0189c

ilvD

Probable dihydroxy-acid dehydratase IlvD (dad)

[48, 58]

Rv0279c

PE_PGRS4

PE-PGRS family protein PE_PGRS4

∙

Rv0383c

Rv0383c

Possible conserved secreted protein

masks sequencing error in H37Rv

[8]

Rv0578c

PE_PGRS7

PE-PGRS family protein PE_PGRS7

∙

Rv0880

Rv0880

Possible MarR-family transcriptional regulatory protein

[48]

Rv0977

PE_PGRS16

PE-PGRS family protein PE_PGRS16

∙

Rv1068c

PE_PGRS20

PE-PGRS family protein PE_PGRS20

∙

Rv1091

PE_PGRS22

PE-PGRS family protein PE_PGRS22

[36, 38] ∙

Rv1095

phoH2

Probable PHOH-like protein PhoH2

Rv1196

PPE18

PPE family protein PPE18

[25, 36] ∙

Rv1386

PE15

PE family protein PE15

∙

Rv1450c

PE_PGRS27

PE-PGRS family protein PE_PGRS27

∙

Rv1802

PPE30

PPE family protein PPE30

SNV instantiates CTGGAG motif

∙

Rv1929c

Rv1929c

Conserved hypothetical protein

Rv2048c

pks12

Polyketide synthase Pks12

Rv2068c

blaC

Class a beta-lactamase BlaC

Rv2069

sigC

RNA polymerase sigma factor, ECF subfamily, SigC

[18, 19]

Rv2098c

PE_PGRS36

PE-PGRS family protein PE_PGRS36

Likely pseudogene

∙

Rv2202c

adoK

Adenosine kinase

Synonymous mutation

Rv2396

PE_PGRS41

PE-PGRS family protein PE_PGRS41

∙

Rv2649

Rv2649

Probable transposase for IS6110

Rv2733c

Rv2733c

Conserved hypothetical alanine, arginine-rich protein

Rv2734

Rv2734

Conserved hypothetical protein

Rv2825c

Rv2825c

Conserved hypothetical protein

Rv3031

Rv3031

Conserved protein

Synonymous mutation

Rv3191c

Rv3191c

Probable transposase

labeled intergenic in H37RaJH

Rv3192

Rv3192

Conserved hypothetical alanine and proline-rich protein

labeled intergenic in H37RaJH

Rv3303c

lpdA

NAD(P)H quinone reductase LpdA

tandem repeat copy number variation

[48]

Rv3350c

PPE56

PPE family protein

∙

Rv3388

PE_PGRS52

PE-PGRS family protein PE_PGRS52

[36] ∙

Rv3389c

htdY

Probable 3-hydroxyacyl-thioester dehydratase HtdY

Rv3507

PE_PGRS53

PE-PGRS family protein PE_PGRS53

[37] ∙

Rv3595c

PE_PGRS59

PE-PGRS family protein PE_PGRS59

[36, 38] ∙

Rv3611

Rv3611

Hypothetical arginine and proline rich protein

One deletion also at ftsH -57bp

(b) Genes with Different H37Ra-specific Variant Profiles in our Assembly

Rv1764

Rv1764

Putative transposase of insertion element IS6110

disrupted by IS6110 in our assembly

Rv3343c

PPE54

PPE family protein

tandem repeat copy number variation

[36] ∙

Rv3508

PE_PGRS54

PE-PGRS family protein PE_PGRS54

[36–38] ∙

Rv3514

PE_PGRS57

PE-PGRS family protein PE_PGRS57

[36, 37] ∙

(c) Genes with High-Confidence Variant Profiles Fully Confirmed by our Assembly

Rv0010c

Rv0010c

Probable conserved membrane protein

Rv0039c

Rv0039c

Possible conserved transmembrane protein

Rv0101

nrp

Probable peptide synthetase Nrp (peptide synthase)

[9, 24]

Rv0635

hadA

(3R)-hydroxyacyl-ACP dehydratase subunit HadA

[33, 38]

Rv0637

hadC

(3R)-hydroxyacyl-ACP dehydratase subunit HadC

[25, 33]

Rv0757

phoP

Member of Two-component response complex PhoPR

[18, 23, 25, 49, 58]

Rv0878c

PPE13

PPE family protein PPE13

[36, 38] ∙

Rv1005c

pabB

Probable para-aminobenzoate synthase component I

[48]

Rv1006

Rv1006

Unknown protein

Rv1021

mazG

NTP Pyrophosphohydrolase, MazG

[31, 32, 48, 58, 60]

Rv1755c

plcD

Probable phospholipase C 4 (fragment) PlcD

[8, 61]

Rv1759c

wag22

PE-PGRS family protein Wag22

[36] ∙

Rv2352c

PPE38

PPE family protein PPE38

exact, adjacent duplication of PPE38

[25, 40] ∙

Rv3879c

espK

ESX-1 secretion-associated protein EspK.

(d) Genes with Variant Profiles Erroneously Declared as H37Ra-specific

Rv2421c†

nadD

Probable nicotinate-nucleotide adenylyltransferase NadD

SNV instantiates CTGGAG motif

[48]

Rv3053c

nrdH

Probable glutaredoxin electron transport component of NRDEF NrdH

[48]