TB-Profiler result

Run: ERR11050531
Summary

Run ID: ERR11050531

Sample name:

Date: 03-04-2023 09:27:18

Number of reads: 8004932

Percentage reads mapped: 99.52

Strain: lineage4.3.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.1 Euro-American (LAM) LAM9 None 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289040 p.Trp68Arg missense_variant 1.0 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 5958 p.Ser240Phe missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.15
mshA 576113 p.Arg256Gly missense_variant 0.26
mshA 576613 c.1266A>C synonymous_variant 0.24
mshA 576616 c.1269G>C synonymous_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.23
pepQ 2860159 p.Ala87Gly missense_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.2
fbiD 3339734 p.Ala206Gly missense_variant 0.56
fbiD 3339746 p.Ala210Gly missense_variant 0.42
fbiD 3339751 p.Ala212Pro missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568431 c.249C>G synonymous_variant 0.21
rpoA 3878597 c.-90G>C upstream_gene_variant 0.26
rpoA 3878641 c.-134C>G upstream_gene_variant 0.83
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245227 c.1995C>T synonymous_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.32
embB 4247016 p.Ser168Trp missense_variant 0.2
embB 4247020 c.507C>G synonymous_variant 0.19
embB 4247468 p.Tyr319Asp missense_variant 1.0
embB 4247515 c.1002C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0