TB-Profiler result

Run: SRR7755706
Summary

Run ID: SRR7755706

Sample name:

Date: 2024-10-04T23:50:12.585711

Number of reads: 2404162

Percentage reads mapped: 54.95

Median coverage: 40.0

Strain: lineage4.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 1.0
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) 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 rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Ser297Ala Uncertain significance Mutation from literature
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 0.91 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin Assoc w R
embB 4247402 p.Ser297Ala missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
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 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
fgd1 491247 c.465C>T synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
ccsA 619969 p.Val27Ile missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R - Interim
amikacin Not assoc w R
rpoC 762965 c.-405T>C upstream_gene_variant 0.2 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 0.22 rifampicin
rpoB 762989 c.3183G>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.33 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.29 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.31 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.61 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472827 n.982G>C non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473193 n.1348G>A non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin
streptomycin
amikacin Uncertain significance
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.66 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.66 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.53 capreomycin Not assoc w R
linezolid 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 2063685 c.1044G>A synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086742 c.-78A>C upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623222 c.1689A>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243225 c.-8C>A upstream_gene_variant 0.96 ethambutol Uncertain significance
embB 4249594 c.3081G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ethA 4326632 p.His281Pro missense_variant 1.0 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 1.0 ethionamide
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