TB-Profiler result

Run: ERR4817463
Summary

Run ID: ERR4817463

Sample name:

Date: 2024-06-18T11:30:47.041744

Number of reads: 5925483

Percentage reads mapped: 95.32

Median coverage: 128.0

Strain: La3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
La3 M.orygis None 0.98
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 rrs n.888G>A Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.430_432delGACinsAT 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance Mutation from literature
ethA 4327042 c.430_432delGACinsAT frameshift_variant&synonymous_variant 0.98 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
dnaA 1501 p.Ile501Leu missense_variant 0.98 isoniazid Uncertain significance
gyrB 4966 c.-274C>T upstream_gene_variant 0.98 levofloxacin
moxifloxacin
gyrB 5516 p.Ile93Val missense_variant 0.98 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6109 c.870G>A synonymous_variant 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrB 6717 p.Ile493Thr missense_variant 0.96 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 7775 c.474C>T synonymous_variant 0.96 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8930 c.1629C>T synonymous_variant 0.97 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13315 p.Ser82Pro missense_variant 0.98 isoniazid Not assoc w R
Rv0010c 13441 p.Thr40Ala missense_variant 0.98 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.98 isoniazid Not assoc w R
Rv0010c 13572 c.-14G>A upstream_gene_variant 0.98 isoniazid Uncertain significance
fgd1 490661 c.-122_-121insGCGAGC upstream_gene_variant 0.9 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
fgd1 491749 p.Leu323Phe missense_variant 0.98 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.98 ethionamide
rpoB 762352 c.2557_2562dupGACGAG conservative_inframe_insertion 0.86 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778086 c.394dupG frameshift_variant 0.97 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.98 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
sigE 1364345 c.-68A>G upstream_gene_variant 0.98 pyrazinamide
embR 1417554 c.-207C>G upstream_gene_variant 0.95 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.89 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.89 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.91 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.89 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.89 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.89 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.89 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.88 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 0.84 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrl 1476664 n.3007T>G non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673680 c.-522C>G upstream_gene_variant 0.97 ethionamide Uncertain significance
isoniazid Not assoc w R
rpsA 1834363 c.822G>A synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
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 2062922 p.Ile603Val missense_variant 0.99 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154707 p.Val469Leu missense_variant 0.99 isoniazid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.98 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2169279 c.1312_1333delAACAATGGTGTCTTTTACCGTG frameshift_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170669 c.-57G>A upstream_gene_variant 0.96 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.98 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289978 c.-737T>G upstream_gene_variant 0.96 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.98 isoniazid
ahpC 2726378 c.186T>A synonymous_variant 0.99 isoniazid Not assoc w R
folC 2746391 p.Val403Ala missense_variant 0.94 para-aminosalicylic_acid
Rv2752c 3067009 c.-818A>G upstream_gene_variant 0.97 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyX 3067812 p.Gln45Arg missense_variant 0.98 para-aminosalicylic_acid
thyA 3074494 c.-81_-24delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG upstream_gene_variant 0.98 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.96 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.98 cycloserine
Rv3083 3448783 p.Val94Ile missense_variant 0.98 ethionamide Uncertain significance
Rv3236c 3612694 c.423T>C synonymous_variant 0.97 pyrazinamide Not assoc w R - Interim
Rv3236c 3613600 c.-484G>A upstream_gene_variant 0.93 pyrazinamide
lpqB 3624350 c.561G>T synonymous_variant 0.96 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.96 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624593 c.318G>A synonymous_variant 0.98 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3641584 p.Val17Ala missense_variant 0.97 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
clpC1 4039853 c.852G>A synonymous_variant 0.98 pyrazinamide Not assoc w R - Interim
clpC1 4040945 c.-241G>A upstream_gene_variant 0.97 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.96 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4239276 c.-587_-586insTGGCCGCCGCCATCGGGT upstream_gene_variant 0.91 ethambutol Uncertain significance
embC 4239301 c.-562G>C upstream_gene_variant 0.13 ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.97 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4244154 p.Thr308Ala missense_variant 0.96 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.96 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.99 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.97 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.99 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.98 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.99 ethambutol Not assoc w R
ethA 4328211 c.-738A>G upstream_gene_variant 0.98 ethionamide
whiB6 4338269 p.Gly85Ser missense_variant 0.96 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407800 p.Val135Met missense_variant 0.97 streptomycin Uncertain significance