TB-Profiler result

Run: SRR29772760
Summary

Run ID: SRR29772760

Sample name:

Date: 2024-10-03T23:31:36.403867

Number of reads: 3640364

Percentage reads mapped: 99.18

Median coverage: 105.5

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 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.Leu430Pro Assoc w R
p.Asn437Asp Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn Assoc w R
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
gyrA 7581 p.Asp94Asn missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761095 p.Leu430Pro missense_variant 0.98 rifampicin Assoc w R
rpoB 761115 p.Asn437Asp missense_variant 0.98 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol 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
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 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 1.0 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.98 ethionamide Uncertain significance
rpoB 761848 p.Cys681Ser missense_variant 0.12 rifampicin
rpoB 761852 c.2046C>G synonymous_variant 0.12 rifampicin
rpoB 761858 c.2052G>C synonymous_variant 0.12 rifampicin
rpoB 761873 c.2067A>C synonymous_variant 0.15 rifampicin
rpoB 761885 c.2079T>C synonymous_variant 0.17 rifampicin
rpoB 761906 c.2100C>G synonymous_variant 0.15 rifampicin
rpoB 761909 c.2103T>C synonymous_variant 0.15 rifampicin
rpoB 761912 c.2106T>C synonymous_variant 0.15 rifampicin
rpoB 761915 p.Asp703Glu missense_variant 0.15 rifampicin
rpoB 761916 p.Asp704Asn missense_variant 0.15 rifampicin
rpoB 761948 c.2142G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761999 c.2193G>C synonymous_variant 0.14 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762017 c.2211A>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765784 c.2415C>G synonymous_variant 0.1 rifampicin
rpoC 765811 c.2442T>G synonymous_variant 0.1 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.1 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.11 rifampicin
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 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpR5 779048 p.Val20Ala missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834189 c.648G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834195 c.654G>C synonymous_variant 0.11 pyrazinamide
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
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide 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 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877668 c.840A>G synonymous_variant 0.1 rifampicin
rpoA 3877686 c.822A>G synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoA 3877743 c.765T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.1 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.12 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTTG synonymous_variant 0.14 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.12 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.11 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.11 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.1 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.1 pyrazinamide Not assoc w R - Interim
clpC1 4039481 c.1224T>C synonymous_variant 0.11 pyrazinamide
clpC1 4039484 c.1221T>C synonymous_variant 0.11 pyrazinamide
clpC1 4039487 c.1218G>C synonymous_variant 0.11 pyrazinamide
clpC1 4040363 c.342A>C synonymous_variant 0.11 pyrazinamide
clpC1 4040369 c.336C>G synonymous_variant 0.11 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
ethA 4326855 p.Arg207Cys missense_variant 1.0 ethionamide 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 1.0 streptomycin Not assoc w R