TB-Profiler result

Run: SRR3086405
Summary

Run ID: SRR3086405

Sample name:

Date: 04-04-2023 05:01:30

Number of reads: 874451

Percentage reads mapped: 98.99

Strain: lineage4.3.3

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289099 p.Lys48Thr missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4247708 p.Asn399Asp missense_variant 0.11 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 0.86 ethionamide
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
fgd1 491690 p.Trp303Leu missense_variant 0.22
mshA 576516 p.Val390Ala missense_variant 1.0
ccsA 620154 c.264C>A synonymous_variant 0.11
rpoC 764467 c.1098C>A synonymous_variant 0.2
rpoC 764914 p.Met515Ile missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766068 p.Glu900Gly missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776291 c.2190G>T synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.18
fabG1 1673392 c.-48G>T upstream_gene_variant 0.13
rpsA 1834210 c.669C>T synonymous_variant 0.11
rpsA 1834417 c.876G>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168790 p.Pro608His missense_variant 0.18
PPE35 2170016 c.597C>A synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2221798 p.Phe456Tyr missense_variant 0.13
Rv1979c 2222419 p.Asp249Gly missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289356 c.-115G>A upstream_gene_variant 0.13
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726064 c.-129C>A upstream_gene_variant 0.11
folC 2746199 p.Val467Asp missense_variant 0.14
folC 2747013 p.Pro196Thr missense_variant 0.12
Rv2752c 3065757 c.435C>A synonymous_variant 0.12
thyX 3068008 c.-63G>T upstream_gene_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074351 p.Gly41Cys missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3640956 c.-579G>T upstream_gene_variant 0.14
ddn 3987246 p.Asp135Asn missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240774 c.912C>A synonymous_variant 0.22
embC 4241470 c.1608C>T synonymous_variant 0.14
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243392 p.Asn54Asp missense_variant 1.0
embA 4243812 p.Arg194Trp missense_variant 0.13
embB 4246595 p.Trp28Gly missense_variant 0.11
ubiA 4269541 p.Pro98His missense_variant 0.18
ubiA 4269731 p.Ala35Ser missense_variant 1.0
ethR 4327922 p.Gln125Arg missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407986 p.Gly73Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0