TB-Profiler result

Run: SRR1140753
Summary

Run ID: SRR1140753

Sample name:

Date: 2024-03-25T19:06:48.539551

Number of reads: 685641

Percentage reads mapped: 18.82

Median coverage: 12.0

Strain: lineage4.3.4.2.1

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.95
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 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.His445Asp Assoc w R
isoniazid
ethambutol
pyrazinamide
streptomycin 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
cycloserine
ethionamide ethA c.440_779del Assoc w R
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 761139 p.His445Asp missense_variant 0.86 rifampicin Assoc w R
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance Mutation from literature
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
amikacin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.43 amikacin Assoc w R
kanamycin Assoc w R
capreomycin Assoc w R
ethA 4326694 c.440_779del frameshift_variant 1.0 ethionamide Assoc w R
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
gyrB 6140 p.Val301Leu missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
rpoB 762887 c.3081G>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 762896 c.-474G>C upstream_gene_variant 0.46 rifampicin
rpoB 762899 c.3093G>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoB 762917 c.3111C>G synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.63 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 762980 c.-390T>C upstream_gene_variant 0.58 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 0.58 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.73 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>C synonymous_variant 0.41 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.38 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.37 rifampicin
rpoC 763537 c.168C>T synonymous_variant 0.35 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 763550 p.Tyr61Ala missense_variant 0.46 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoC 763585 c.216C>G synonymous_variant 0.66 rifampicin
rpoC 763621 c.252C>T synonymous_variant 0.58 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoC 763642 c.273G>C synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>T synonymous_variant 0.56 rifampicin
rpoC 763696 c.327T>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.75 rifampicin Not assoc w R - Interim
rpoC 764578 c.1209C>G synonymous_variant 0.37 rifampicin
rpoC 764581 c.1212T>C synonymous_variant 0.68 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.7 rifampicin
rpoC 764587 c.1218C>G synonymous_variant 0.41 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.45 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.27 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.65 rifampicin Not assoc w R
rpoC 764998 c.1629G>C synonymous_variant 0.32 rifampicin
rpoC 765007 c.1638T>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 765008 c.1639T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 765014 p.Ala549Pro missense_variant 0.35 rifampicin
rpoC 765019 c.1650A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
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
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472092 n.247C>T non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472120 n.275G>A non_coding_transcript_exon_variant 0.56 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.7 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 0.81 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472245 n.400C>A non_coding_transcript_exon_variant 0.59 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.73 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.44 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472380 n.535G>A non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472484 n.639A>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472506 n.661A>T non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472572 n.727T>A non_coding_transcript_exon_variant 0.64 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.37 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.81 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.77 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.75 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 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473047 n.1202C>T non_coding_transcript_exon_variant 0.55 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.52 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473157 n.1312C>T non_coding_transcript_exon_variant 0.69 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.68 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.71 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.48 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 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473288 n.1443delCinsAGTTT non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473298 n.1453A>G non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473698 n.41G>A non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1473699 n.42A>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid
rrl 1473719 n.62G>A non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1473721 n.64G>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1473722 n.65G>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1473731 n.74T>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1473833 n.176_177insT non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473884 n.227C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1473887 n.230T>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473889 n.232G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1473898 n.241C>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474155 n.498G>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1474171 n.514C>G non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474287 n.630T>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1474355 n.698A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1474359 n.702C>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474406 n.749T>C non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474806 n.1149A>G non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1474822 n.1165G>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1474927 n.1271delC non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475104 n.1447T>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475109 n.1452C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475116 n.1459G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475124 n.1467A>T non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475536 n.1879C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475538 n.1881T>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475548 n.1891C>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475549 n.1892T>C non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475655 n.1998T>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475696 n.2039T>A non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid
rrl 1475697 n.2040C>T non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.66 capreomycin Uncertain significance
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475989 n.2332T>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475990 n.2333G>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid Uncertain significance
rrl 1476105 n.2450delA non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.71 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.68 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.69 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.45 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.85 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.69 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid
rrl 1476519 n.2862C>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476534 n.2877A>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.64 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476594 n.2937C>A non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1476603 n.2946G>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476616 n.2959A>G non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.56 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476628 n.2971T>G non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid
rrl 1476661 n.3004A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834327 c.786G>T synonymous_variant 0.44 pyrazinamide
rpsA 1834348 c.807T>G synonymous_variant 0.3 pyrazinamide
rpsA 1834354 c.813G>C synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
rpsA 1834357 c.816T>C synonymous_variant 0.3 pyrazinamide
rpsA 1834361 c.820_822delTTGinsCC frameshift_variant&missense_variant 0.32 pyrazinamide Uncertain significance
rpsA 1834366 c.825A>G synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
rpsA 1834378 c.837T>G synonymous_variant 0.3 pyrazinamide
rpsA 1834387 c.846C>T synonymous_variant 0.31 pyrazinamide
rpsA 1834395 p.Arg285Gln missense_variant 0.39 pyrazinamide
rpsA 1834408 c.867C>G synonymous_variant 0.32 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.27 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.29 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide 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 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
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R