TB-Profiler result

Run: SRR10380209
Summary

Run ID: SRR10380209

Sample name:

Date: 02-04-2023 17:30:42

Number of reads: 3161573

Percentage reads mapped: 99.75

Strain: lineage4.3.3;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 0.1
lineage4 Euro-American LAM;T;S;X;H None 0.89
lineage4.3 Euro-American (LAM) mainly-LAM None 0.87
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.13
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.09
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.88
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
thyX 3067961 c.-16C>T upstream_gene_variant 0.13 para-aminosalicylic_acid
thyA 3073808 p.Arg222Gly missense_variant 0.14 para-aminosalicylic_acid
embB 4249583 p.Asp1024Asn missense_variant 0.88 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
gyrB 6579 p.Ser447Tyr missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.89
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.15
mshA 575907 p.Ala187Val missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.24
ccsA 620625 p.Ile245Met missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.22
rpoC 764841 p.Ile491Ser missense_variant 0.86
rpoC 764995 c.1626C>G synonymous_variant 0.81
rpoC 765612 p.His748Pro missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.88
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.86
PPE35 2167926 p.Leu896Ser missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.86
folC 2746340 p.Ala420Val missense_variant 0.87
pepQ 2860159 p.Ala87Gly missense_variant 0.19
thyA 3073868 p.Thr202Ala missense_variant 0.89
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
fbiB 3641810 c.276G>C synonymous_variant 0.14
rpoA 3878637 c.-130G>C upstream_gene_variant 0.24
rpoA 3878641 c.-134C>G upstream_gene_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 0.86
clpC1 4038968 c.1737G>A synonymous_variant 0.92
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.15
embA 4246287 p.Asn1019Asp missense_variant 0.16
aftB 4267647 p.Asp397Gly missense_variant 0.1
ubiA 4269089 p.Ala249Thr missense_variant 0.18
ethA 4326339 p.Asn379Asp missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 0.86