TB-Profiler result

Run: SRR6511607
Summary

Run ID: SRR6511607

Sample name:

Date: 04-04-2023 15:14:50

Number of reads: 1180403

Percentage reads mapped: 99.69

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 1.0
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2288850 c.390_391dupGG frameshift_variant 0.95 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7642 p.Gly114Asp missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491426 p.Ala215Val missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407108 p.Ala78Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474705 n.1048T>A non_coding_transcript_exon_variant 0.12
rrl 1474764 n.1107G>A non_coding_transcript_exon_variant 0.11
rrl 1474767 n.1110A>G non_coding_transcript_exon_variant 0.11
rrl 1475205 n.1548G>A non_coding_transcript_exon_variant 0.11
rrl 1476409 n.2752T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156011 p.Gly34Val missense_variant 1.0
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289358 c.-118delG upstream_gene_variant 0.18
pncA 2289731 c.-490A>G upstream_gene_variant 0.11
kasA 2518709 c.597delA frameshift_variant 0.12
ahpC 2726622 p.Ile144Val missense_variant 0.1
ribD 2987379 p.Gln181Lys missense_variant 0.11
ribD 2987384 c.546C>A synonymous_variant 0.12
thyX 3067502 c.444C>T synonymous_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474896 p.Asp297Gly missense_variant 0.11
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039991 c.714G>A synonymous_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245831 p.Pro867Ser missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408102 p.Gly34Val missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0