TB-Profiler result

Run: SRR4034202
Summary

Run ID: SRR4034202

Sample name:

Date: 04-04-2023 06:38:03

Number of reads: 1386546

Percentage reads mapped: 99.69

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
katG 2155740 c.371delG frameshift_variant 0.12 isoniazid, 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
gyrB 5060 c.-180G>T upstream_gene_variant 0.15
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 5566 c.327C>T synonymous_variant 0.15
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
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 576330 p.Leu328Pro missense_variant 0.14
rpoB 760624 p.Arg273Pro missense_variant 0.13
rpoB 761282 c.1476C>T synonymous_variant 0.11
rpoB 762107 c.2301C>A synonymous_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777520 p.Thr321Pro missense_variant 0.13
mmpL5 778920 c.-441delG upstream_gene_variant 0.15
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 1.0
rrl 1473484 n.-174C>A upstream_gene_variant 0.15
rrl 1475085 n.1428C>A non_coding_transcript_exon_variant 0.18
inhA 1674952 p.Pro251Ala missense_variant 0.12
rpsA 1833359 c.-183T>C upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.22
katG 2154699 p.Gln471His missense_variant 0.12
katG 2155620 c.492G>T synonymous_variant 0.11
PPE35 2168786 c.1827G>T synonymous_variant 0.12
Rv1979c 2222534 p.Ala211Thr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448897 c.396delC frameshift_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840984 c.436delC frameshift_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240693 c.831T>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326702 p.Arg258Trp missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0