TB-Profiler result

Run: SRR14801325
Summary

Run ID: SRR14801325

Sample name:

Date: 2024-03-26T21:32:45.819203

Number of reads: 4521039

Percentage reads mapped: 80.08

Median coverage: 141.0

Strain: lineage4.2.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download JSON
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 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin 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 embA c.-12C>T Uncertain significance Mutation from literature
embB p.Ser297Ala Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Gly88Cys Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Gly88Cys Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin 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
gyrA 7563 p.Gly88Cys missense_variant 0.99 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
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 0.98 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.94 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 ethionamide Assoc w R Alias fabG1_c.-15C>T
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)
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.98 ethambutol Uncertain significance Mutation from literature
embB 4247402 p.Ser297Ala missense_variant 0.98 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 0.99 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 0.99 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
ccsA 619969 p.Val27Ile missense_variant 0.99 capreomycin Not assoc w R - Interim
amikacin Not assoc w R
kanamycin Uncertain significance
rpoB 761102 c.1296A>G synonymous_variant 0.11 rifampicin
rpoC 763534 c.165T>C synonymous_variant 0.11 rifampicin
rpoC 763537 c.168C>G synonymous_variant 0.11 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 0.98 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 0.97 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471985 n.140T>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471991 n.146T>C non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471997 n.152T>C non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471998 n.153G>T non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472005 n.160T>G non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.32 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 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.1 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472486 n.641A>G non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472494 n.649A>T non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472507 n.662C>T non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472508 n.663T>C non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472673 n.828T>C non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472685 n.840G>T non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472686 n.841G>C non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472687 n.842A>G non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472793 n.948A>C non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472836 n.991G>A non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472840 n.995A>C non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472844 n.999C>A non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472845 n.1000G>A non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472850 n.1005T>C non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472862 n.1017T>C non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472863 n.1018T>C non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472873 n.1028C>T non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472875 n.1030T>G non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124_1125insAGCCCTT non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472972 n.1127T>G non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473062 n.1217T>G non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473120 n.1275C>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.37 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 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473201 n.1356A>T non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.42 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 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474476 n.819C>G non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474483 n.826C>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1474497 n.840G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474528 n.871T>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474529 n.872A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474540 n.883T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474541 n.884G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474662 n.1005C>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474688 n.1031G>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1474753 n.1096_1097delACinsG non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474777 n.1120T>G non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474896 n.1239A>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475740 n.2083G>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475761 n.2104C>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475763 n.2106_2109delCAAGinsGATTCGTCCA non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475788 n.2131C>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1475883 n.2226A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475982 n.2325G>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476015 n.2358G>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476032 n.2375C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476058 n.2401T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476255 n.2598A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476529 n.2872A>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
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 0.98 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 0.98 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102029 c.1014G>A synonymous_variant 1.0 ethionamide
delamanid
isoniazid
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
pncA 2287932 c.463_*748del stop_lost&conservative_inframe_deletion&splice_region_variant 0.99 pyrazinamide
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 0.99 ethambutol Not assoc w R - Interim
ethA 4326632 p.His281Pro missense_variant 0.99 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.98 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