TB-Profiler result

Run: SRR13861198

Summary

Run ID: SRR13861198

Sample name:

Date: 2024-04-15T14:54:12.129536

Number of reads: 2261635

Percentage reads mapped: 56.6

Median coverage: 77.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive


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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
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 442 p.Pro148Ala missense_variant 1.0 isoniazid
gyrB 6667 p.Gln476His missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 7289 c.-13_-12insT upstream_gene_variant 1.0 levofloxacin
moxifloxacin
rpoB 760214 p.Asn136Lys missense_variant 1.0 rifampicin
Rv1129c 1253228 p.Asp436Ala missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1253885 p.Lys217Arg missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1304005 p.Pro359Ser missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
sigE 1364782 p.Val124Leu missense_variant 1.0 pyrazinamide
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471943 n.98T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472075 n.230A>C non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473066 n.1221A>T non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473370 n.1525T>C non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.32 capreomycin Not assoc w R
linezolid Uncertain significance
fabG1 1673813 p.Arg125Leu missense_variant 1.0 ethionamide
isoniazid
inhA 1674784 p.Arg195Gly missense_variant 1.0 ethionamide
isoniazid
bacA 2064693 p.Trp12Cys missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
ndh 2101793 p.Trp417* stop_gained 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
PPE35 2169624 p.Gly330Asp missense_variant 1.0 pyrazinamide
kasA 2519223 p.Thr370Ile missense_variant 0.99 isoniazid
ahpC 2726213 c.21C>T synonymous_variant 0.99 isoniazid
Rv2477c 2783213 p.Ala277Val missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin
streptomycin Uncertain significance
levofloxacin
kanamycin
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2477c 2783662 p.Glu127Asp missense_variant 1.0 ethambutol
moxifloxacin Uncertain significance
streptomycin
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2477c 2784275 c.-234dupC upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ribD 2987016 p.Gly60Arg missense_variant 0.99 para-aminosalicylic_acid
Rv2680 2996618 p.Trp172Arg missense_variant 1.0 capreomycin
Rv2681 2997515 c.777T>G synonymous_variant 1.0 capreomycin
Rv2681 2997779 c.1041C>G synonymous_variant 1.0 capreomycin
Rv2752c 3065644 p.Thr183Ser missense_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066590 c.-399A>G upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3074595 c.-124C>A upstream_gene_variant 1.0 para-aminosalicylic_acid
lpqB 3624763 p.Val50Leu missense_variant 1.0 bedaquiline
rifampicin
lpqB 3625054 c.-144C>G upstream_gene_variant 1.0 bedaquiline
rifampicin
alr 3841581 c.-161T>A upstream_gene_variant 1.0 cycloserine
embC 4242810 p.Leu983Gln missense_variant 1.0 ethambutol
embB 4246553 p.Arg14Trp missense_variant 1.0 ethambutol
embB 4248920 p.Val803Met missense_variant 1.0 ethambutol Uncertain significance
embB 4249551 p.Arg1013Leu missense_variant 1.0 ethambutol
ethA 4326296 p.Leu393Gln missense_variant 1.0 ethionamide
gid 4408480 c.-278G>C upstream_gene_variant 1.0 streptomycin