TB-Profiler result

Run: SRR6480617
Summary

Run ID: SRR6480617

Sample name:

Date: 04-04-2023 14:46:57

Number of reads: 3132673

Percentage reads mapped: 99.71

Strain: lineage4.3;lineage4.1.2.1

Drug-resistance: Other

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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 0.85
lineage4.1 Euro-American T;X;H None 0.14
lineage4.1.2 Euro-American T;H None 0.16
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.17
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
pncA 2288997 p.His82Arg missense_variant 0.76 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9074 c.1773G>A synonymous_variant 0.88
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.14
mshA 575679 p.Asn111Ser missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 0.86
rpoC 765150 p.Gly594Glu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406785 p.Leu186Phe missense_variant 0.84
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.15
thyA 3073806 c.666C>G synonymous_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 0.89
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612176 p.Arg314Gln missense_variant 0.85
clpC1 4038287 c.2418C>T synonymous_variant 0.79
clpC1 4038857 c.1848C>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.87