TB-Profiler result

Run: ERR4812270
Summary

Run ID: ERR4812270

Sample name:

Date: 01-04-2023 11:58:07

Number of reads: 827449

Percentage reads mapped: 99.51

Strain: lineage4.3.4.1

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 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4408022 c.180delA frameshift_variant 1.0 streptomycin
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
mshA 576108 p.Ala254Gly missense_variant 0.31
mshA 576778 c.1431G>A synonymous_variant 0.14
ccsA 619883 c.-8G>C upstream_gene_variant 0.67
ccsA 620250 c.360C>A synonymous_variant 0.2
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765590 p.Arg741Ser missense_variant 0.96
rpoC 767047 p.Phe1226Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406835 p.Gly169Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834378 c.837T>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918268 p.Ala110Asp missense_variant 0.13
Rv1979c 2223123 c.42G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859819 c.600G>A synonymous_variant 0.15
pepQ 2859984 c.435A>G synonymous_variant 0.5
ribD 2986648 c.-191T>G upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087278 p.Gln153His missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474899 p.Gly298Asp missense_variant 0.25
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641647 p.Pro38Leu missense_variant 0.13
fbiB 3641664 p.Asp44Asn missense_variant 0.12
fbiB 3641933 c.399C>T synonymous_variant 0.4
fbiB 3642134 c.600G>T synonymous_variant 1.0
alr 3841254 p.Ala56Asp missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244806 p.Leu525Gln missense_variant 0.22
embA 4244875 p.Pro548Gln missense_variant 0.33
embB 4247033 p.Ser174Arg missense_variant 0.33
embB 4247644 c.1131G>C synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0