TB-Profiler result

Run: SRR13068977
Summary

Run ID: SRR13068977

Sample name:

Date: 03-04-2023 08:12:00

Number of reads: 179285

Percentage reads mapped: 99.42

Strain:

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
lineage4.4.1.1 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2154100 p.Ser671* stop_gained 0.4 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289186 p.Leu19Arg missense_variant 1.0 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
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 5896 c.657C>G synonymous_variant 0.67
gyrB 6429 p.Glu397Val missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619699 c.-192G>A upstream_gene_variant 0.33
ccsA 620304 p.Trp138Cys missense_variant 0.18
rpoC 764666 p.Gly433Ser missense_variant 1.0
rpoC 765623 p.Arg752Cys missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777661 p.Ala274Thr missense_variant 0.4
mmpL5 778137 p.Arg115Ile missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781835 c.276T>C synonymous_variant 0.4
fbiC 1303058 p.Glu43Val missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674651 c.450C>T synonymous_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154102 c.2010C>T synonymous_variant 0.4
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289263 c.-22C>T upstream_gene_variant 0.29
pncA 2289601 c.-360T>G upstream_gene_variant 0.2
ahpC 2726039 c.-154C>A upstream_gene_variant 0.33
ahpC 2726423 c.231C>T synonymous_variant 0.5
ahpC 2726737 p.Asp182Val missense_variant 0.29
folC 2746649 p.Ala317Val missense_variant 1.0
ribD 2987368 p.Val177Gly missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448641 c.138C>T synonymous_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3612696 p.Arg141Cys missense_variant 0.22
clpC1 4038237 p.Thr823Asn missense_variant 0.17
clpC1 4039287 p.Leu473His missense_variant 0.29
clpC1 4039383 p.Ala441Val missense_variant 0.18
embC 4240661 p.Trp267Arg missense_variant 0.15
embA 4243571 c.339G>A synonymous_variant 0.4
embA 4245389 c.2157C>T synonymous_variant 0.2
embB 4247055 p.Leu181Gln missense_variant 0.29
embB 4247223 p.Trp237* stop_gained 0.22
aftB 4267329 p.Arg503Leu missense_variant 0.5
aftB 4269690 c.-854C>T upstream_gene_variant 0.33
ubiA 4269811 c.22delC frameshift_variant 0.33
ethA 4327208 p.Ala89Val missense_variant 0.2
ethA 4327247 p.Ala76Asp missense_variant 1.0
ethR 4327282 c.-267G>A upstream_gene_variant 0.18
ethA 4327361 p.Arg38Leu missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0