TB-Profiler result

Run: SRR6797302
Summary

Run ID: SRR6797302

Sample name:

Date: 04-04-2023 16:05:30

Number of reads: 1024236

Percentage reads mapped: 99.47

Strain: 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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rrs 1472362 n.517C>T non_coding_transcript_exon_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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 763031 c.-339T>G upstream_gene_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406824 p.Thr173Pro missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673357 c.-83G>A upstream_gene_variant 0.27
fabG1 1673359 c.-81T>C upstream_gene_variant 0.27
fabG1 1673361 c.-79C>G upstream_gene_variant 0.23
fabG1 1673380 c.-60C>G upstream_gene_variant 0.42
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169366 p.Ser416Ile missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.57
PPE35 2170053 p.Thr187Ser missense_variant 0.57
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726130 c.-63A>C upstream_gene_variant 1.0
folC 2746405 c.1193delT frameshift_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
aftB 4267798 c.1039C>T synonymous_variant 1.0
whiB6 4338514 p.Tyr3Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0