TB-Profiler result

Run: ERR108512
Summary

Run ID: ERR108512

Sample name:

Date: 31-03-2023 11:20:48

Number of reads: 4546365

Percentage reads mapped: 99.68

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 0.96
lineage4.3 Euro-American (LAM) mainly-LAM None 0.9
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.08
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.1
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.91
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 761139 p.His445Tyr missense_variant 0.88 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.11 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.94 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.94 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
eis 2715342 c.-10G>A upstream_gene_variant 0.13 kanamycin
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 8040 p.Gly247Ser missense_variant 0.91
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.9
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.92
fbiC 1304962 p.Trp678Gly missense_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.12
rpsA 1834836 p.Met432Thr missense_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.15
katG 2156196 c.-85C>T upstream_gene_variant 0.92
PPE35 2169320 p.Leu431Phe missense_variant 0.2
PPE35 2170756 c.-144G>A upstream_gene_variant 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.91
folC 2746340 p.Ala420Val missense_variant 0.88
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.98
clpC1 4038968 c.1737G>A synonymous_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>T upstream_gene_variant 0.75
embA 4243346 c.114A>G synonymous_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.94