TB-Profiler result

Run: ERR1194807
Summary

Run ID: ERR1194807

Sample name:

Date: 31-03-2023 12:34:14

Number of reads: 786402

Percentage reads mapped: 99.5

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 1.0
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
mshA 576021 p.Ile225Thr missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 763005 p.Cys1067Arg missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763821 p.Leu151Pro missense_variant 0.11
rpoC 766645 p.Glu1092Asp missense_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 776479 p.Ala668Thr missense_variant 0.15
mmpL5 779265 c.-785A>G upstream_gene_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800796 c.-13A>G upstream_gene_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472408 n.563A>G non_coding_transcript_exon_variant 0.12
inhA 1674980 p.Ala260Asp missense_variant 0.15
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
katG 2154911 p.Pro401Thr missense_variant 0.25
katG 2155448 p.Ala222Pro missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168428 c.2184delG frameshift_variant 0.11
PPE35 2169144 p.Val490Glu missense_variant 0.25
PPE35 2169511 p.Asn368Tyr missense_variant 0.29
Rv1979c 2222015 p.Val384Leu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726303 c.111T>A synonymous_variant 0.19
folC 2747004 p.Ile199Phe missense_variant 0.2
Rv2752c 3065500 p.Gly231Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087007 p.Gln63Leu missense_variant 0.22
fbiD 3339428 p.Ala104Gly missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.25
whiB7 3568627 p.Leu18Ser missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642263 c.732delG frameshift_variant 0.13
fbiB 3642685 p.Leu384Ser missense_variant 0.12
alr 3840756 p.Ala222Val missense_variant 0.12
embA 4242316 c.-917C>T upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267894 p.Ile315Phe missense_variant 0.38
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