TB-Profiler result

Run: SRR14164943
Summary

Run ID: SRR14164943

Sample name:

Date: 03-04-2023 10:09:11

Number of reads: 644418

Percentage reads mapped: 98.62

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
ahpC 2726119 c.-74G>A upstream_gene_variant 1.0 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
mshA 576108 p.Ala254Gly missense_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778282 p.Asp67His missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.4
rrl 1474018 n.361G>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168733 p.Thr627Asn missense_variant 0.11
PPE35 2169526 p.Asn363Asp missense_variant 0.12
PPE35 2169548 c.1065A>T synonymous_variant 0.13
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2221749 c.1416C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073880 p.Glu198Lys missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3877919 p.Glu197Lys missense_variant 1.0
embC 4242228 p.Gly789Asp missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245461 c.2229C>T synonymous_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0