TB-Profiler result

Run: ERR10762297
Summary

Run ID: ERR10762297

Sample name:

Date: 2024-04-15T11:07:34.301730

Number of reads: 6202355

Percentage reads mapped: 83.89

Median coverage: 181.0

Strain: lineage4.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.99
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser428Thr Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Ser431Thr Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Ser297Ala Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
rrs n.799C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
eis c.-12C>T Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761089 p.Ser428Thr missense_variant 0.11 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761098 p.Ser431Thr missense_variant 0.11 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761155 p.Ser450Leu missense_variant 0.92 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.95 streptomycin Assoc w R
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance Mutation from literature
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.21 amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.16 capreomycin Assoc w R
kanamycin Assoc w R
amikacin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin Assoc w R
embB 4247402 p.Ser297Ala missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491247 c.465C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
ccsA 619969 p.Val27Ile missense_variant 1.0 capreomycin Not assoc w R - Interim
amikacin Not assoc w R
kanamycin Uncertain significance
rpoB 761027 c.1221A>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761051 c.1245G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761064 p.Ala420Ser missense_variant 0.12 rifampicin Uncertain significance
rpoB 761102 c.1296A>G synonymous_variant 0.11 rifampicin
rpoB 762176 c.2370T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoB 763007 p.Cys1067Trp missense_variant 0.1 rifampicin
rpoB 763014 p.Met1070Leu missense_variant 0.12 rifampicin
rpoB 763017 p.Gln1071Glu missense_variant 0.12 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.15 rifampicin Not assoc w R
rpoB 763040 c.3234C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763053 c.3247_3249delTTGinsCC frameshift_variant&missense_variant 0.15 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763074 p.Thr1090Val missense_variant 0.13 rifampicin
rpoB 763077 p.Val1091Pro missense_variant 0.13 rifampicin
rpoB 763094 c.3288G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763504 c.135C>G synonymous_variant 0.12 rifampicin
rpoC 763507 c.138G>C synonymous_variant 0.12 rifampicin
rpoC 763528 c.159G>C synonymous_variant 0.13 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.13 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.13 rifampicin
rpoC 763537 c.168C>T synonymous_variant 0.14 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763633 c.264T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.14 rifampicin
rpoC 763660 c.291T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763669 c.300C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.13 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.13 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764620 c.1251G>C synonymous_variant 0.16 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764644 c.1275G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764706 p.Leu446Gln missense_variant 0.17 rifampicin Uncertain significance
rpoC 764716 c.1347G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 0.96 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 1.0 linezolid
atpE 1460953 c.-92T>C upstream_gene_variant 1.0 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472674 n.829T>C non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472685 n.840G>A non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473127 n.1282G>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473292 n.1447_1449delGGAinsTGGG non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474664 n.1007G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.24 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>A non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475740 n.2083G>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475761 n.2104_2106delCGCinsT non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475766 n.2109G>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475788 n.2131C>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476213 n.2556G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476288 n.2631T>C non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.24 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834024 c.483G>C synonymous_variant 0.1 pyrazinamide
rpsA 1834336 c.795C>G synonymous_variant 0.11 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.11 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.99 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086742 c.-78A>C upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623222 c.1689A>G synonymous_variant 0.99 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ethA 4326632 p.His281Pro missense_variant 1.0 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin