TB-Profiler result

Run: SRR6257107
Summary

Run ID: SRR6257107

Sample name:

Date: 04-04-2023 13:26:34

Number of reads: 831229

Percentage reads mapped: 100.0

Strain: lineage2.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326463 c.1010delT frameshift_variant 1.0 ethionamide, ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620853 c.963G>T synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764918 p.Val517Leu missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302966 c.36G>T synonymous_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1460909 c.-136C>A upstream_gene_variant 0.12
atpE 1461212 c.168C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471773 n.-73G>T upstream_gene_variant 0.12
rpsA 1833368 c.-174G>T upstream_gene_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169021 p.Gly531Glu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.2
pepQ 2859888 p.Glu177Asp missense_variant 0.11
thyX 3068102 c.-157T>C upstream_gene_variant 0.11
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339343 p.Gly76Cys missense_variant 0.13
fbiD 3339747 c.630G>T synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475207 p.Asp401Tyr missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642772 p.Asp413Ala missense_variant 0.22
embC 4240446 p.Pro195Gln missense_variant 0.12
embC 4240984 p.Ser374Arg missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242882 p.Pro1007His missense_variant 0.12
embC 4242910 p.Phe1016Leu missense_variant 0.17
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243464 p.Ala78Ser missense_variant 0.12
embB 4247639 c.1127delC frameshift_variant 0.11
embB 4248290 p.Val593Leu missense_variant 0.12
embB 4248667 c.2154C>T synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268434 p.Ala135Ser missense_variant 0.11
ubiA 4270022 c.-189C>A upstream_gene_variant 0.11
ethA 4328393 c.-920T>C upstream_gene_variant 0.11
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0