TB-Profiler result

Run: SRR15399224
Summary

Run ID: SRR15399224

Sample name:

Date: 03-04-2023 14:10:40

Number of reads: 4997121

Percentage reads mapped: 99.7

Strain: lineage4.4.1.2;lineage4.3.2

Drug-resistance: HR-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 0.4
lineage4.4 Euro-American S;T None 0.57
lineage4.3.2 Euro-American (LAM) LAM3 None 0.41
lineage4.4.1 Euro-American (S-type) S;T None 0.58
lineage4.4.1.2 Euro-American T1 None 0.58
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
katG 2155168 p.Ser315Asn missense_variant 0.4 isoniazid
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
rpoC 764995 c.1626C>G synonymous_variant 0.45
rpoC 766051 c.2682G>A synonymous_variant 0.58
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.67
katG 2156483 c.-372C>G upstream_gene_variant 0.41
PPE35 2167770 p.Ser948Ile missense_variant 0.62
PPE35 2169840 p.Gly258Asp missense_variant 0.65
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519131 c.1017G>T synonymous_variant 0.4
pepQ 2860213 p.Pro69Leu missense_variant 0.6
thyA 3073868 p.Thr202Ala missense_variant 0.34
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.45
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878627 c.-120T>G upstream_gene_variant 0.25
ddn 3986910 p.Arg23Trp missense_variant 0.44
clpC1 4038287 c.2418C>T synonymous_variant 0.49
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249012 c.2499G>A synonymous_variant 0.61
whiB6 4338289 p.Gly78Glu missense_variant 0.56
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.34