TB-Profiler result

Run: SRR6046736
Summary

Run ID: SRR6046736

Sample name:

Date: 2024-10-04T18:21:20.911330

Number of reads: 2442645

Percentage reads mapped: 98.01

Median coverage: 80.0

Strain: La3;lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.24
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.23
lineage2.2 East-Asian (Beijing) RD105;RD207 0.25
La3 M.orygis None 0.66
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
gyrB 4966 c.-274C>T upstream_gene_variant 0.73 levofloxacin
moxifloxacin
gyrB 5516 p.Ile93Val missense_variant 0.77 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 5920 c.681C>T synonymous_variant 0.79 levofloxacin
moxifloxacin
gyrB 6109 c.870G>A synonymous_variant 0.79 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrB 6717 p.Ile493Thr missense_variant 0.78 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 8930 c.1629C>T synonymous_variant 0.7 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 0.72 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 0.82 isoniazid Not assoc w R
Rv0010c 13441 p.Thr40Ala missense_variant 0.78 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.8 isoniazid Not assoc w R
fgd1 490661 c.-122_-121insGCGAGC upstream_gene_variant 0.85 pretomanid
delamanid
clofazimine
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
fgd1 491749 p.Leu323Phe missense_variant 0.78 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
mshA 575907 p.Ala187Val missense_variant 0.3 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.25 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.2 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.21 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.69 ethionamide
rpoB 762352 c.2557_2562dupGACGAG conservative_inframe_insertion 0.6 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.24 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.23 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 778086 c.394dupG frameshift_variant 0.73 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 778588 p.Gln106His missense_variant 0.17 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.25 bedaquiline
clofazimine
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 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.76 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
sigE 1364345 c.-68A>G upstream_gene_variant 0.64 pyrazinamide
sigE 1364706 c.294G>A synonymous_variant 0.33 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.28 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.71 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1475539 n.1882A>G non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476664 n.3007T>G non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673680 c.-522C>G upstream_gene_variant 0.69 isoniazid Not assoc w R
ethionamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.29 pyrazinamide Not assoc w R - Interim
rpsA 1834363 c.822G>A synonymous_variant 0.65 pyrazinamide Not assoc w R - Interim
rpsA 1834433 p.Pro298Ser missense_variant 0.69 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.58 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154707 p.Val469Leu missense_variant 0.81 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 0.68 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 0.81 pyrazinamide Uncertain significance
PPE35 2170669 c.-57G>A upstream_gene_variant 0.79 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.82 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289978 c.-737T>G upstream_gene_variant 0.78 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.75 isoniazid
ahpC 2726378 c.186T>A synonymous_variant 0.78 isoniazid Not assoc w R
folC 2746391 p.Val403Ala missense_variant 0.68 para-aminosalicylic_acid
Rv2752c 3067009 c.-818A>G upstream_gene_variant 0.67 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyX 3067812 p.Gln45Arg missense_variant 0.79 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.83 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.82 cycloserine
Rv3083 3448783 p.Val94Ile missense_variant 0.71 ethionamide Uncertain significance
Rv3236c 3612694 c.423T>C synonymous_variant 0.79 pyrazinamide Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 0.28 pyrazinamide Not assoc w R - Interim
Rv3236c 3613600 c.-484G>A upstream_gene_variant 0.7 pyrazinamide
lpqB 3624350 c.561G>T synonymous_variant 0.69 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.83 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624593 c.318G>A synonymous_variant 0.8 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.3 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3641584 p.Val17Ala missense_variant 0.72 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
clpC1 4039853 c.852G>A synonymous_variant 0.71 pyrazinamide Not assoc w R - Interim
clpC1 4040945 c.-241G>A upstream_gene_variant 0.75 pyrazinamide
panD 4044134 p.Asp50Asn missense_variant 0.7 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4239276 c.-587_-586insTGGCCGCCGCCATCGGGT upstream_gene_variant 0.44 ethambutol Uncertain significance
embC 4239301 c.-562G>C upstream_gene_variant 0.12 ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.71 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.28 ethambutol Not assoc w R
embA 4244154 p.Thr308Ala missense_variant 0.57 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.6 ethambutol Not assoc w R
embA 4244762 c.1530C>T synonymous_variant 0.69 ethambutol Not assoc w R - Interim
embB 4246712 p.Val67Leu missense_variant 0.63 ethambutol Uncertain significance
embB 4246864 c.351C>T synonymous_variant 0.66 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.74 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.23 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.75 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.74 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.56 ethambutol Not assoc w R
ethA 4327042 p.Asp144Asn missense_variant 0.67 ethionamide Uncertain significance
ethA 4328211 c.-738A>G upstream_gene_variant 0.74 ethionamide
whiB6 4338269 p.Gly85Ser missense_variant 0.77 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.33 streptomycin Not assoc w R