TB-Profiler result

Run: ERR11466014
Summary

Run ID: ERR11466014

Sample name:

Date: 2024-04-14T23:03:33.996047

Number of reads: 3682839

Percentage reads mapped: 99.76

Median coverage: 93.0

Strain: lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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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 1.0
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 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
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
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 10 p.Asp4His missense_variant 1.0 isoniazid Uncertain significance
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 761027 c.1221A>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762236 c.2430G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762254 c.2448T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762257 c.2451C>G synonymous_variant 0.15 rifampicin
rpoB 762266 c.2460T>C synonymous_variant 0.18 rifampicin
rpoB 762275 c.2469C>G synonymous_variant 0.19 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>C synonymous_variant 0.14 rifampicin
rpoC 763534 c.165T>C synonymous_variant 0.17 rifampicin
rpoC 763537 c.168C>G synonymous_variant 0.17 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763633 c.264T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.15 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.13 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.13 rifampicin
rpoC 764536 c.1167G>C synonymous_variant 0.16 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764578 c.1209C>G synonymous_variant 0.12 rifampicin
rpoC 764581 c.1212T>C synonymous_variant 0.12 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.12 rifampicin
rpoC 764587 c.1218C>G synonymous_variant 0.13 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766393 c.3024C>T synonymous_variant 1.0 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 777128 c.1353A>G synonymous_variant 0.11 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.32 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 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473062 n.1217T>G non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475028 n.1371G>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833769 c.228C>G synonymous_variant 0.12 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
katG 2155410 c.702G>C synonymous_variant 0.1 isoniazid Not assoc w R - Interim
PPE35 2169902 c.709_711delCTGinsTC frameshift_variant&synonymous_variant 0.18 pyrazinamide Uncertain significance
PPE35 2169910 p.Asn235Tyr missense_variant 0.22 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
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4039610 c.1095G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039787 c.918G>C synonymous_variant 0.11 pyrazinamide
clpC1 4039790 c.915C>G synonymous_variant 0.12 pyrazinamide
clpC1 4039904 c.801A>G synonymous_variant 0.12 pyrazinamide
glpK 4138643 c.1113A>G synonymous_variant 0.13 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4138646 c.1110G>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138734 p.Ser341Thr missense_variant 0.11 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
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