TB-Profiler result

Run: ERR4815121
Summary

Run ID: ERR4815121

Sample name:

Date: 2024-04-15T11:40:11.239474

Number of reads: 3909053

Percentage reads mapped: 85.67

Median coverage: 80.0

Strain: lineage4.6.2.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 1.0
lineage4.6.2 Euro-American RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) RD726 1.0
lineage4 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
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.115delC Assoc w R
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
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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
amikacin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.29 capreomycin Assoc w R
kanamycin Assoc w R
amikacin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin 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
dnaA 519 c.519C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
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 761537 c.1731C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761552 c.1746G>C synonymous_variant 0.16 rifampicin
rpoB 761554 p.Val583Ala missense_variant 0.15 rifampicin Uncertain significance
rpoB 761561 c.1755C>G synonymous_variant 0.16 rifampicin
rpoB 761570 c.1764T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761600 c.1794T>C synonymous_variant 0.21 rifampicin
rpoB 761606 c.1800C>G synonymous_variant 0.24 rifampicin
rpoB 761612 c.1806G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.11 rifampicin Uncertain significance
rpoB 762209 c.2403C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762212 c.2406G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762245 c.2439G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762249 c.2443C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762254 c.2448T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762266 c.2460T>C synonymous_variant 0.23 rifampicin
rpoC 763504 c.135C>A synonymous_variant 0.17 rifampicin
rpoC 763507 c.138G>C synonymous_variant 0.2 rifampicin
rpoC 763528 c.159G>T synonymous_variant 0.22 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.22 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.23 rifampicin
rpoC 763537 c.168C>G synonymous_variant 0.23 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 763621 c.252delCinsTTCG conservative_inframe_insertion&synonymous_variant 0.18 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763642 c.273G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 764524 c.1155C>T synonymous_variant 0.11 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764560 c.1191T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.1 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764665 c.1296C>G synonymous_variant 0.16 rifampicin
rpoC 764668 c.1299C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764677 c.1308C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764706 p.Leu446Gln missense_variant 0.18 rifampicin Uncertain significance
rpoC 764713 c.1344G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764722 c.1353G>C synonymous_variant 0.17 rifampicin
rpoC 764746 c.1377G>C synonymous_variant 0.12 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.12 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
mmpL5 778298 c.183G>A synonymous_variant 1.0 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781769 p.Glu70Asp missense_variant 0.1 streptomycin
rpsL 781796 p.Met79Ile missense_variant 0.1 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.52 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.52 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 0.58 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 0.63 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472791 n.946G>T non_coding_transcript_exon_variant 0.53 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.49 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 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473065 n.1220C>A non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.33 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 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473127 n.1282G>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473274 n.1429C>A non_coding_transcript_exon_variant 0.61 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473292 n.1447_1450delGGAGinsTGGAA non_coding_transcript_exon_variant 0.47 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473831 n.174_175delGCinsAGA non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1473844 n.187C>T non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473870 n.213G>A non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473871 n.214T>C non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473887 n.230T>A non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474135 n.478G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474141 n.484G>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474142 n.485C>G non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474179 n.522C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474182 n.525C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474202 n.545T>A non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474641 n.984G>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475655 n.1998T>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475752 n.2095C>G non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1475753 n.2096C>A non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid
rrl 1475771 n.2114A>C non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.38 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.36 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.36 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.75 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.78 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.56 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid
rpsA 1833676 c.135A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833679 c.138G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833685 c.144G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833697 c.156C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833700 c.159C>T synonymous_variant 0.18 pyrazinamide
rpsA 1833721 c.180A>G synonymous_variant 0.21 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.18 pyrazinamide
rpsA 1833733 c.192C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833734 p.Ala65Ser missense_variant 0.14 pyrazinamide
rpsA 1833997 c.456G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834024 c.483G>C synonymous_variant 0.22 pyrazinamide
rpsA 1834034 c.493_495delATCinsGG frameshift_variant&missense_variant 0.21 pyrazinamide Uncertain significance
rpsA 1834040 p.Lys167Gln missense_variant 0.24 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834090 c.549G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834096 c.555G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834102 c.561T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834286 p.Ser249Gly missense_variant 0.13 pyrazinamide
rpsA 1834294 c.753G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834298 p.Gln253Glu missense_variant 0.12 pyrazinamide
rpsA 1834303 c.762T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834307 c.766_768delGACinsCG frameshift_variant&missense_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834327 c.786G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834330 c.789C>G synonymous_variant 0.12 pyrazinamide
rpsA 1834447 c.906C>G synonymous_variant 0.11 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.11 pyrazinamide
rpsA 1834456 c.915T>C synonymous_variant 0.11 pyrazinamide
rpsA 1834459 c.918G>C synonymous_variant 0.1 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.1 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.1 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.1 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
bacA 2063187 c.1542C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.96 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2996208 p.Ala35Asp missense_variant 1.0 capreomycin Uncertain significance
Rv2681 2997605 c.867A>C synonymous_variant 1.0 capreomycin
Rv3083 3448567 p.His22Asp missense_variant 1.0 ethionamide Uncertain significance
clpC1 4039826 c.879C>G synonymous_variant 0.12 pyrazinamide
clpC1 4039831 c.874T>C synonymous_variant 0.12 pyrazinamide
clpC1 4039838 c.865_867delCTGinsAC frameshift_variant&missense_variant 0.13 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039871 c.834C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039875 p.Asn277Arg missense_variant 0.14 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 1.0 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
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