TB-Profiler result

Run: ERR4818781
Summary

Run ID: ERR4818781

Sample name:

Date: 17-08-2022 08:21:01

Number of reads: 697304

Percentage reads mapped: 99.78

Strain: lineage4.3.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289054 p.Asp63Gly missense_variant 0.18 pyrazinamide
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 5801 p.Glu188Lys missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9077 c.1776C>T synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491221 p.Arg147Cys missense_variant 0.15
mshA 576531 p.Val395Ala missense_variant 0.1
rpoB 759786 c.-21G>A upstream_gene_variant 0.12
rpoB 760484 c.678A>G synonymous_variant 0.12
rpoB 761868 p.Asp688Tyr missense_variant 0.12
rpoB 762171 p.Glu789Lys missense_variant 0.17
rpoB 763089 p.Lys1095Glu missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765439 p.Lys690Asn missense_variant 0.12
rpoC 767147 p.Ala1260Thr missense_variant 0.2
mmpL5 775628 c.2853G>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776157 p.Asp775Gly missense_variant 0.18
mmpS5 778752 p.Asp52Asn missense_variant 0.17
mmpL5 779364 c.-884C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781492 c.-68G>A upstream_gene_variant 0.12
rplC 800895 c.89delA frameshift_variant 0.13
fbiC 1302995 p.Asn22Ile missense_variant 0.15
Rv1258c 1407362 c.-22G>A upstream_gene_variant 0.12
embR 1416326 p.Ile341Thr missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471663 n.-183C>T upstream_gene_variant 0.18
inhA 1674769 p.Ala190Thr missense_variant 0.14
ndh 2102308 c.735G>T synonymous_variant 0.18
katG 2154782 p.Ala444Ser missense_variant 0.15
katG 2155866 c.246A>G synonymous_variant 0.13
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2170687 c.-75C>T upstream_gene_variant 0.12
Rv1979c 2222943 c.222A>T synonymous_variant 0.12
Rv1979c 2222968 p.Ala66Val missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715266 p.Ser23Gly missense_variant 0.12
folC 2746340 p.Ala420Val missense_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ribD 2987480 c.642G>A synonymous_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3087393 p.Ala192Thr missense_variant 0.14
ald 3087673 c.857delC frameshift_variant 0.12
fbiD 3339730 p.Pro205Thr missense_variant 0.11
Rv3083 3449177 p.Lys225Arg missense_variant 0.12
Rv3083 3449587 p.Gly362Arg missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474793 p.Gly263* stop_gained 0.12
fbiB 3641699 c.165A>G synonymous_variant 0.1
ddn 3986981 c.138C>T synonymous_variant 0.15
clpC1 4038222 p.Ala828Asp missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038540 p.Leu722Gln missense_variant 0.18
clpC1 4038923 c.1782A>G synonymous_variant 0.11
clpC1 4038968 c.1737G>A synonymous_variant 1.0
clpC1 4039586 c.1119G>A synonymous_variant 0.12
clpC1 4040565 p.Lys47Arg missense_variant 0.1
panD 4044072 c.210C>T synonymous_variant 0.18
embC 4241838 p.Trp659* stop_gained 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243192 c.-40delT upstream_gene_variant 1.0
embA 4243702 p.Gly157Asp missense_variant 0.12
embB 4248814 c.2301G>T synonymous_variant 0.13
embB 4249207 c.2694G>A synonymous_variant 0.12
embB 4249336 c.2823C>A synonymous_variant 0.15
aftB 4268121 p.Thr239Ile missense_variant 0.15
aftB 4268358 p.Gln160Arg missense_variant 0.1
ubiA 4268947 p.Gly296Val missense_variant 0.12
aftB 4269369 c.-533G>T upstream_gene_variant 0.11
ubiA 4270003 c.-170G>T upstream_gene_variant 0.13
ethR 4327123 c.-426G>C upstream_gene_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 1.0