TB-Profiler result

Run: ERR1199093
Summary

Run ID: ERR1199093

Sample name:

Date: 31-03-2023 12:34:40

Number of reads: 593692

Percentage reads mapped: 99.67

Strain: lineage4.6.1.2

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
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.2 Euro-American T2 RD724 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 761100 p.Gln432Glu missense_variant 1.0 rifampicin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Gly missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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 5092 c.-148A>T upstream_gene_variant 0.21
gyrB 6142 c.903G>T synonymous_variant 0.3
gyrB 6705 p.Glu489Val missense_variant 0.4
gyrB 6749 p.Ala504Ser missense_variant 0.5
gyrB 7072 p.Lys611Asn missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7570 p.Ala90Gly missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7897 p.Asp199Ala missense_variant 0.25
gyrA 9280 p.Val660Gly missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 763428 p.Ile20Asn missense_variant 0.15
rpoC 764810 p.Pro481Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776226 p.Glu752Val missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303219 p.Leu97Ile missense_variant 0.17
fbiC 1303519 p.Ser197Arg missense_variant 0.25
embR 1416410 p.Leu313Arg missense_variant 1.0
atpE 1460965 c.-80A>T upstream_gene_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473307 n.1462A>T non_coding_transcript_exon_variant 0.17
rrl 1475373 n.1716G>A non_coding_transcript_exon_variant 1.0
rrl 1475472 n.1815T>A non_coding_transcript_exon_variant 0.75
rrl 1475822 n.2165A>T non_coding_transcript_exon_variant 0.25
rrl 1475886 n.2229T>A non_coding_transcript_exon_variant 0.6
rrl 1476371 n.2714A>T non_coding_transcript_exon_variant 0.5
rrl 1476441 n.2784T>G non_coding_transcript_exon_variant 0.25
inhA 1674799 p.Ser200Cys missense_variant 0.17
tlyA 1917826 c.-114A>C upstream_gene_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102356 c.687T>G synonymous_variant 0.18
katG 2154323 p.Tyr597Asn missense_variant 0.23
katG 2154705 c.1407C>G synonymous_variant 0.15
katG 2156403 c.-292A>C upstream_gene_variant 0.14
PPE35 2168447 p.Gln722His missense_variant 0.33
PPE35 2168631 p.Asn661Ser missense_variant 1.0
PPE35 2168681 p.Phe644Leu missense_variant 0.4
PPE35 2169725 p.Asn296Lys missense_variant 0.38
PPE35 2169880 p.Phe245Ile missense_variant 0.22
PPE35 2169917 c.696T>A synonymous_variant 0.38
Rv1979c 2222596 p.Val190Gly missense_variant 0.22
Rv1979c 2223064 p.Leu34Gln missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290020 c.-779T>A upstream_gene_variant 0.29
eis 2714878 p.Asp152Ala missense_variant 0.18
pepQ 2859563 p.Tyr286Asp missense_variant 0.17
pepQ 2860249 p.Asp57Ala missense_variant 0.22
pepQ 2860324 p.Tyr32Phe missense_variant 0.14
pepQ 2860592 c.-174T>A upstream_gene_variant 0.67
Rv2752c 3065836 p.Tyr119Phe missense_variant 0.25
Rv2752c 3065920 p.Pro91Leu missense_variant 1.0
Rv2752c 3065995 p.His66Leu missense_variant 0.17
thyA 3074318 p.Phe52Ile missense_variant 0.29
ald 3086749 c.-71T>A upstream_gene_variant 0.55
Rv3083 3448741 p.Ser80Ala missense_variant 0.43
Rv3083 3449227 p.Phe242Leu missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612327 p.Thr264Ala missense_variant 0.25
fbiA 3640449 c.-94T>A upstream_gene_variant 0.25
fbiA 3640502 c.-41C>A upstream_gene_variant 0.29
alr 3840529 p.Thr298Ser missense_variant 0.44
rpoA 3878031 c.477T>A synonymous_variant 0.4
rpoA 3878300 p.Lys70* stop_gained 0.25
ddn 3987215 c.372A>G synonymous_variant 1.0
clpC1 4038634 p.Glu691Lys missense_variant 0.17
clpC1 4040409 p.Gly99Val missense_variant 0.43
clpC1 4040604 p.Leu34His missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 0.95
embA 4244396 c.1164T>G synonymous_variant 0.14
embA 4244508 p.Leu426Val missense_variant 0.27
embA 4244905 p.Val558Gly missense_variant 0.25
embA 4245020 c.1788T>G synonymous_variant 0.2
embA 4245055 p.Thr608Asn missense_variant 1.0
embB 4248665 p.Phe718Val missense_variant 0.14
embB 4249016 p.Tyr835Asn missense_variant 0.33
embB 4249785 p.Pro1091Gln missense_variant 0.33
aftB 4267365 p.Met491Lys missense_variant 0.22
aftB 4268874 c.-38T>G upstream_gene_variant 0.23
aftB 4269471 c.-635C>A upstream_gene_variant 0.27
ethA 4326171 p.Thr435Ala missense_variant 0.33
ethA 4327451 p.Val8Gly missense_variant 0.5
ethR 4328092 p.Thr182Pro missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408093 p.Gly37Val missense_variant 1.0
gid 4408444 c.-242A>C upstream_gene_variant 0.57