TB-Profiler result

Run: ERR4831796
Summary

Run ID: ERR4831796

Sample name:

Date: 01-04-2023 21:07:32

Number of reads: 1187827

Percentage reads mapped: 98.54

Strain: lineage2.2.1

Drug-resistance: HR-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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747151 p.Ser150Gly missense_variant 1.0 para-aminosalicylic_acid
embC 4240785 p.Gly308Asp missense_variant 0.11 ethambutol
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 575567 c.223delA frameshift_variant 0.11
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576174 p.Pro276Gln missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620841 c.951G>T synonymous_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777213 p.Ala423Gly missense_variant 0.11
mmpL5 777410 p.Ile357Met missense_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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 2170170 p.Val148Ala missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518603 c.489G>C synonymous_variant 0.15
kasA 2519207 p.Gly365Ser missense_variant 0.2
pepQ 2860228 p.Ala64Asp missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448988 p.Arg162Pro missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0
ddn 3987268 p.Arg142His missense_variant 0.13
clpC1 4038534 p.Arg724Leu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.93
embA 4243605 p.Val125Leu missense_variant 0.13
embA 4245181 p.Phe650Cys missense_variant 0.11
embA 4245549 p.Lys773Glu missense_variant 0.5
embB 4247084 p.Asp191Asn missense_variant 0.15
embB 4247794 c.1281G>C synonymous_variant 0.11
embB 4249411 c.2898G>T synonymous_variant 0.11
aftB 4267476 p.Ser454Leu missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268624 c.213C>A synonymous_variant 0.13
ethA 4326337 p.Asn379Lys 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