TB-Profiler result

Run: SRR13861241
Summary

Run ID: SRR13861241

Sample name:

Date: 2024-04-15T05:25:12.066655

Number of reads: 1499799

Percentage reads mapped: 75.06

Median coverage: 50.0

Strain: lineage4.9

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 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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 c.1700delT Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rrs n.888G>A Uncertain significance Mutation from literature
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance Mutation from literature
katG 2154411 c.1700delT frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
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
gyrA 7523 c.222C>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7949 c.648G>T synonymous_variant 0.92 levofloxacin
moxifloxacin
gyrA 8123 p.Leu274Phe missense_variant 0.89 levofloxacin Uncertain significance
moxifloxacin
gyrA 8198 c.897T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9768 p.Gly823Cys missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0565c 657349 p.Glu41Val missense_variant 0.99 ethionamide
rpoC 763696 c.327T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763708 c.339G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763709 c.340C>T synonymous_variant 0.14 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.15 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.17 rifampicin
rpoC 763734 p.Pro122Leu missense_variant 0.83 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.15 rifampicin
rpoC 765970 c.2601C>T synonymous_variant 0.12 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 766672 c.3303T>C synonymous_variant 0.13 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.15 rifampicin
rpoC 766738 c.3369G>T synonymous_variant 0.15 rifampicin
rpoC 766750 c.3381C>G synonymous_variant 0.13 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766801 c.3432C>A synonymous_variant 0.12 rifampicin
rpoC 766861 c.3492G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpsL 781892 c.333A>G synonymous_variant 0.13 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.13 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.14 streptomycin
Rv1129c 1253309 p.His409Pro missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472678 n.833_834delTTinsGCC non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472684 n.839_845delGGGATCCinsA non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.57 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476640 n.2983C>A non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
tsnR 1853566 c.-40C>T upstream_gene_variant 1.0 linezolid
tlyA 1918034 p.Val32Ala missense_variant 1.0 capreomycin
bacA 2064615 p.Leu38Phe missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
katG 2155918 p.Ala65Val missense_variant 1.0 isoniazid
PPE35 2168767 p.Ser616Gly missense_variant 1.0 pyrazinamide
PPE35 2170815 c.-203C>G upstream_gene_variant 1.0 pyrazinamide
Rv1979c 2222377 p.Val263Gly missense_variant 1.0 clofazimine
bedaquiline
Rv2477c 2783077 c.966T>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783092 c.951A>G synonymous_variant 0.15 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2783095 c.948C>G synonymous_variant 0.16 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R
amikacin Not assoc w R - Interim
Rv2477c 2783104 c.939C>A synonymous_variant 0.84 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783110 c.933C>A synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783116 c.927T>C synonymous_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783140 c.903C>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783185 c.858G>C synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ribD 2986993 p.Gly52Val missense_variant 1.0 para-aminosalicylic_acid
Rv2752c 3065787 c.405G>C synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv3083 3448649 p.Arg49Pro missense_variant 1.0 ethionamide
Rv3236c 3613067 p.Val17Gly missense_variant 1.0 pyrazinamide
Rv3236c 3613315 c.-199T>G upstream_gene_variant 1.0 pyrazinamide
lpqB 3624166 p.Met249Leu missense_variant 0.15 bedaquiline
rifampicin
lpqB 3624172 p.Val247Ile missense_variant 0.15 bedaquiline
rifampicin
lpqB 3624173 c.738A>C synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3624188 c.723G>C synonymous_variant 0.14 bedaquiline
rifampicin
lpqB 3624191 c.720C>G synonymous_variant 0.14 bedaquiline
rifampicin
lpqB 3624200 c.711A>G synonymous_variant 0.14 bedaquiline
rifampicin
lpqB 3624209 c.702A>C synonymous_variant 0.15 bedaquiline
rifampicin
mtrB 3626903 c.-290T>C upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrA 3626912 c.438T>C synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
fbiA 3640435 c.-108A>C upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fbiB 3642614 c.1080C>T synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiB 3642620 c.1086T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
rpoA 3878982 c.-475A>T upstream_gene_variant 0.96 rifampicin
clpC1 4039842 c.862_863insT frameshift_variant 0.98 pyrazinamide
panD 4044103 p.Ile60Ser missense_variant 0.98 pyrazinamide
embC 4240900 c.1038A>G synonymous_variant 0.13 ethambutol
embC 4241035 c.1173G>A synonymous_variant 0.12 ethambutol
embC 4241137 c.1275G>C synonymous_variant 0.13 ethambutol
embC 4241158 c.1296T>C synonymous_variant 0.13 ethambutol
embC 4241161 c.1299C>G synonymous_variant 0.13 ethambutol Not assoc w R - Interim
embA 4245031 p.Arg600Gln missense_variant 0.98 ethambutol
gid 4408218 c.-16G>T upstream_gene_variant 1.0 streptomycin