TB-Profiler result

Run: SRR22528570
Summary

Run ID: SRR22528570

Sample name:

Date: 04-04-2023 04:18:58

Number of reads: 769165

Percentage reads mapped: 99.63

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155109 p.Ile335Val missense_variant 0.17 isoniazid
katG 2155168 p.Ser315Thr missense_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 7516 p.Lys72Met missense_variant 0.13
gyrA 7555 p.His85Arg missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576123 p.Leu259Arg missense_variant 0.12
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
rpsL 781467 c.-93G>C upstream_gene_variant 0.11
fbiC 1303701 c.771C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472119 n.274G>T non_coding_transcript_exon_variant 0.13
rrl 1475352 n.1695T>C non_coding_transcript_exon_variant 0.11
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.14
rpsA 1833490 c.-52C>G upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103167 c.-125A>T upstream_gene_variant 0.13
ndh 2103199 c.-157G>T upstream_gene_variant 0.15
katG 2156410 c.-299T>C upstream_gene_variant 0.12
PPE35 2168287 p.Ile776Val missense_variant 0.12
PPE35 2170705 c.-93T>C upstream_gene_variant 0.11
Rv1979c 2222214 c.951C>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
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 3474342 p.Leu112Phe missense_variant 0.15
Rv3236c 3612853 c.264C>T synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246558 c.45G>T synonymous_variant 0.2
embB 4246582 c.69T>G synonymous_variant 0.13
whiB6 4338252 p.Phe90Leu missense_variant 0.53
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0