TB-Profiler result

Run: SRR3732582
Summary

Run ID: SRR3732582

Sample name:

Date: 04-04-2023 05:36:10

Number of reads: 1563387

Percentage reads mapped: 99.54

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 0.99
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289090 p.His51Arg missense_variant 1.0 pyrazinamide
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762224 c.2418C>T synonymous_variant 0.13
rpoB 762418 p.Arg871Leu missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766487 p.Pro1040Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406242 p.Ala367Ser missense_variant 0.12
Rv1258c 1407537 c.-197G>A upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472340 n.495C>A non_coding_transcript_exon_variant 0.4
rrs 1472633 n.788C>A non_coding_transcript_exon_variant 0.2
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.33
rpsA 1834683 p.Ala381Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154455 p.Glu553* stop_gained 0.12
katG 2154715 p.Gly466Val missense_variant 0.13
PPE35 2170058 c.555G>T synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289645 c.-404G>T upstream_gene_variant 0.18
kasA 2518117 c.3G>T synonymous_variant 0.17
kasA 2518416 p.Pro101Leu missense_variant 0.13
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519173 c.1059C>A synonymous_variant 0.25
folC 2746226 p.Gly458Val missense_variant 0.14
pepQ 2859560 p.Gly287Cys missense_variant 0.12
pepQ 2859607 p.Arg271Leu missense_variant 0.12
ribD 2987206 p.Ser123Tyr missense_variant 0.15
thyX 3067301 p.Cys215* stop_gained 0.12
thyX 3067667 c.279G>A synonymous_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339409 p.Ala98Thr missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612693 c.424C>A synonymous_variant 0.12
fbiA 3640359 c.-184C>A upstream_gene_variant 0.15
fbiA 3641234 p.Ala231Val missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039381 p.Gln442Lys missense_variant 0.14
panD 4044265 p.Leu6Pro missense_variant 0.1
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244750 c.1518C>A synonymous_variant 0.14
embA 4244782 p.Arg517His missense_variant 0.14
embA 4246202 p.Gln990His missense_variant 0.17
embB 4247145 p.Ser211Phe missense_variant 0.12
embB 4247628 p.Arg372Leu missense_variant 0.12
embB 4247888 p.Gly459Cys missense_variant 0.12
embB 4249781 p.Ser1090Pro missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0