TB-Profiler result

Run: ERR4818851
Summary

Run ID: ERR4818851

Sample name:

Date: 2024-10-04T19:10:59.682673

Number of reads: 1168188

Percentage reads mapped: 43.37

Median coverage: 26.0

Strain: lineage4.4.1.1

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1 Euro-American (S-type) None 1.0
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 1.0
lineage4.4 Euro-American 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.Ser441Ala Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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 761127 p.Ser441Ala missense_variant 0.31 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
Rv0010c 13452 p.Gly36Val missense_variant 1.0 isoniazid Uncertain significance
rpoB 761054 c.1248G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761058 p.Val418Thr missense_variant 0.33 rifampicin
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.39 rifampicin
rpoB 761096 c.1290G>C synonymous_variant 0.37 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.37 rifampicin
rpoB 761132 c.1326G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761600 c.1794T>C synonymous_variant 0.31 rifampicin
rpoB 761612 c.1806G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762197 c.2391C>G synonymous_variant 0.34 rifampicin
rpoB 762206 c.2400C>G synonymous_variant 0.44 rifampicin
rpoB 762212 c.2406G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 762233 p.Pro810Ser missense_variant 0.41 rifampicin
rpoB 762245 c.2439G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 762248 c.2442G>C synonymous_variant 0.43 rifampicin
rpoB 762254 c.2448T>C synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 762863 c.-507T>G upstream_gene_variant 0.25 rifampicin
rpoB 762879 p.Met1025Leu missense_variant 0.43 rifampicin Uncertain significance
rpoB 762887 c.3081G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 762896 c.-474G>C upstream_gene_variant 0.47 rifampicin
rpoC 762926 c.-444C>G upstream_gene_variant 0.46 rifampicin
rpoB 762929 c.3123G>T synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 762938 c.-432G>C upstream_gene_variant 0.47 rifampicin
rpoC 762944 c.-426C>T upstream_gene_variant 0.37 rifampicin
rpoC 763468 c.99G>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 763483 c.114G>C synonymous_variant 0.53 rifampicin
rpoC 763486 c.117T>C synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 763492 c.123G>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 763507 c.138G>C synonymous_variant 0.68 rifampicin
rpoC 763528 c.159G>C synonymous_variant 0.64 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.62 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.62 rifampicin
rpoC 763537 c.168C>G synonymous_variant 0.66 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoC 763550 p.Tyr61Ala missense_variant 0.65 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 763578 p.Phe70Tyr missense_variant 0.54 rifampicin
rpoC 763585 c.216C>G synonymous_variant 0.49 rifampicin
rpoC 763589 p.Ile74Val missense_variant 0.48 rifampicin
rpoC 763606 c.237C>A synonymous_variant 0.42 rifampicin
rpoC 763615 c.246G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 763618 c.249C>T synonymous_variant 0.46 rifampicin
rpoC 763622 p.Ala85Ser missense_variant 0.51 rifampicin Uncertain significance
rpoC 763636 c.267T>C synonymous_variant 0.56 rifampicin
rpoC 763642 c.273G>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoC 763647 p.Gly93Ala missense_variant 0.59 rifampicin
rpoC 763655 p.Glu96Lys missense_variant 0.57 rifampicin
rpoC 763660 c.291T>C synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 763669 c.300C>G synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 763708 c.339G>C synonymous_variant 0.5 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.4 rifampicin
rpoC 763724 p.Asp119Asn missense_variant 0.4 rifampicin
rpoC 763729 c.360G>C synonymous_variant 0.37 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.4 rifampicin
rpoC 763735 c.366G>C synonymous_variant 0.4 rifampicin
rpoC 763751 p.Ile128Val missense_variant 0.4 rifampicin
rpoC 763765 c.396T>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>C synonymous_variant 0.29 rifampicin
rpoC 764549 p.Pro394Val missense_variant 0.3 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764572 c.1203G>C synonymous_variant 0.32 rifampicin
rpoC 764575 c.1206T>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.31 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.33 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.46 rifampicin
rpoC 764620 c.1251G>C synonymous_variant 0.41 rifampicin
rpoC 764623 c.1254C>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.4 rifampicin
rpoC 764644 c.1275G>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800618 c.-191T>C upstream_gene_variant 0.28 linezolid
rplC 800632 c.-177_-176delATinsTC upstream_gene_variant 0.37 linezolid
rplC 800639 c.-170C>G upstream_gene_variant 0.45 linezolid
rplC 800645 c.-164C>G upstream_gene_variant 0.48 linezolid
rplC 800648 c.-161A>G upstream_gene_variant 0.5 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.36 linezolid
rplC 800667 c.-142_-140delTCGinsAGC upstream_gene_variant 0.42 linezolid
rplC 800672 c.-137G>C upstream_gene_variant 0.42 linezolid
rplC 800693 c.-116A>G upstream_gene_variant 0.34 linezolid
rplC 800703 c.-106T>C upstream_gene_variant 0.25 linezolid
Rv1129c 1254427 c.108G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.82 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472123 n.278A>G non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.95 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.99 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.85 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.89 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.96 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.95 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.98 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.98 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.98 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.99 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.99 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.99 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.99 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.98 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.96 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.96 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.98 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.91 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.91 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.86 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473284 n.1439A>T non_coding_transcript_exon_variant 0.82 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473287 n.1442_1449delCCTCGGGAinsG non_coding_transcript_exon_variant 0.84 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.84 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473314 n.1469A>G non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473782 n.125A>G non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1473783 n.126A>G non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1473788 n.131A>G non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid
rrl 1473797 n.140G>T non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473807 n.150T>C non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid
rrl 1473811 n.154C>T non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1473822 n.165delAinsTG non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid Uncertain significance
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1473840 n.183A>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1474315 n.658A>G non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474355 n.698A>G non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474393 n.736A>G non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474413 n.757_776delCCCACACGCGCATACGCGCG non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1474437 n.781_782delAA non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid
rrl 1474448 n.791T>C non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474634 n.977T>G non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474658 n.1001A>G non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474711 n.1054_1060delGGTGTAAinsCGGGTTGT non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474753 n.1096_1097delACinsG non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.99 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475031 n.1374G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475059 n.1403_1404insTA non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475062 n.1405A>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475065 n.1409_1411delCAA non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475076 n.1419_1422delCCTTinsGCCCTA non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475080 n.1425_1426delCC non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475090 n.1433A>T non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475104 n.1447T>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475124 n.1467A>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475171 n.1514C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475172 n.1515A>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1475754 n.2097G>A non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1475762 n.2105G>C non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1475763 n.2107_2108delAA non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475774 n.2117C>T non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.91 capreomycin
linezolid
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.86 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.89 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476207 n.2550T>C non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.9 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.92 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.92 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476600 n.2943A>C non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476616 n.2959A>G non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.93 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476628 n.2971T>G non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid
rrl 1476633 n.2976A>G non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476664 n.3007T>A non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476668 n.3011C>T non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476675 n.3018C>A non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rpsA 1833641 p.Asn34Asp missense_variant 0.3 pyrazinamide
rpsA 1833646 c.105T>C synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
rpsA 1833652 c.111C>T synonymous_variant 0.39 pyrazinamide
rpsA 1833661 c.120A>G synonymous_variant 0.44 pyrazinamide
rpsA 1833667 c.126C>T synonymous_variant 0.44 pyrazinamide
rpsA 1833668 p.Ile43Val missense_variant 0.47 pyrazinamide
rpsA 1833676 c.135A>G synonymous_variant 0.5 pyrazinamide
rpsA 1833679 c.138G>C synonymous_variant 0.53 pyrazinamide
rpsA 1833685 c.144G>T synonymous_variant 0.58 pyrazinamide
rpsA 1833688 c.147C>T synonymous_variant 0.61 pyrazinamide
rpsA 1833694 c.153G>C synonymous_variant 0.67 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.69 pyrazinamide
rpsA 1833732 p.Pro64Leu missense_variant 0.65 pyrazinamide
rpsA 1833736 c.195C>T synonymous_variant 0.65 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.68 pyrazinamide
rpsA 1833770 p.Asn77Asp missense_variant 0.56 pyrazinamide
rpsA 1833776 p.Val79Ile missense_variant 0.53 pyrazinamide
rpsA 1833781 c.240T>C synonymous_variant 0.46 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.37 pyrazinamide
rpsA 1833893 p.AlaLeu118ArgIle missense_variant 0.4 pyrazinamide
rpsA 1833905 p.Lys122Glu missense_variant 0.35 pyrazinamide
rpsA 1833912 p.Glu124Gly missense_variant 0.39 pyrazinamide
rpsA 1833915 p.Ala125Val missense_variant 0.41 pyrazinamide Uncertain significance
rpsA 1833921 p.Lys127Thr missense_variant 0.41 pyrazinamide
rpsA 1833926 p.Thr129Ser missense_variant 0.5 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.48 pyrazinamide
rpsA 1833952 c.411C>T synonymous_variant 0.48 pyrazinamide
rpsA 1833955 c.414G>C synonymous_variant 0.47 pyrazinamide
rpsA 1833961 c.420C>G synonymous_variant 0.43 pyrazinamide
rpsA 1833994 c.453G>C synonymous_variant 0.4 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.53 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.53 pyrazinamide
rpsA 1834015 c.474G>T synonymous_variant 0.51 pyrazinamide
rpsA 1834024 c.483G>C synonymous_variant 0.5 pyrazinamide
rpsA 1834034 p.Ile165Val missense_variant 0.41 pyrazinamide
rpsA 1834040 p.Lys167Arg missense_variant 0.4 pyrazinamide
rpsA 1834046 p.Ile169Leu missense_variant 0.41 pyrazinamide
rpsA 1834054 c.513C>G synonymous_variant 0.39 pyrazinamide
rpsA 1834063 c.522C>T synonymous_variant 0.45 pyrazinamide
rpsA 1834195 c.654G>C synonymous_variant 0.34 pyrazinamide
rpsA 1834210 c.669C>T synonymous_variant 0.34 pyrazinamide
rpsA 1834213 c.672G>C synonymous_variant 0.34 pyrazinamide
rpsA 1834219 c.678C>G synonymous_variant 0.34 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834225 c.684C>G synonymous_variant 0.33 pyrazinamide
rpsA 1834228 c.687C>T synonymous_variant 0.33 pyrazinamide
rpsA 1834231 c.690T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834234 c.693G>C synonymous_variant 0.33 pyrazinamide
rpsA 1834246 c.705G>C synonymous_variant 0.31 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.4 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.41 pyrazinamide
rpsA 1834285 c.744G>C synonymous_variant 0.37 pyrazinamide
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
ndh 2102990 p.Val18Ala missense_variant 1.0 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040015 p.Ala230Ser missense_variant 0.24 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.25 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.33 pyrazinamide
clpC1 4040045 c.660C>G synonymous_variant 0.37 pyrazinamide Not assoc w R - Interim
clpC1 4040051 c.654C>G synonymous_variant 0.42 pyrazinamide
clpC1 4040057 c.648C>G synonymous_variant 0.42 pyrazinamide
clpC1 4040063 c.642G>C synonymous_variant 0.42 pyrazinamide Not assoc w R - Interim
clpC1 4040066 c.639G>C synonymous_variant 0.4 pyrazinamide
clpC1 4040069 c.636G>C synonymous_variant 0.41 pyrazinamide
clpC1 4040090 c.615T>C synonymous_variant 0.43 pyrazinamide Not assoc w R - Interim
clpC1 4040096 c.609G>C synonymous_variant 0.39 pyrazinamide
clpC1 4040110 c.595C>A synonymous_variant 0.28 pyrazinamide
clpC1 4040114 p.Ile197Met missense_variant 0.28 pyrazinamide
clpC1 4040117 c.588A>G synonymous_variant 0.28 pyrazinamide
clpC1 4040125 p.Glu194Lys missense_variant 0.29 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin