TB-Profiler result

Run: ERR4820796
Summary

Run ID: ERR4820796

Sample name:

Date: 01-04-2023 16:53:00

Number of reads: 635038

Percentage reads mapped: 99.76

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4247469 p.Tyr319Cys missense_variant 0.12 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 5317 c.78C>G synonymous_variant 0.12
gyrB 6070 c.835delT frameshift_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7710 c.409T>C synonymous_variant 0.12
gyrA 8285 c.984C>T synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491483 p.Ser234Tyr missense_variant 0.25
fgd1 491716 p.Ala312Thr missense_variant 0.25
mshA 575542 c.195C>T synonymous_variant 0.17
mshA 575941 c.594G>A synonymous_variant 0.14
ccsA 620695 p.Phe269Leu missense_variant 0.12
rpoB 762166 p.Gly787Asp missense_variant 0.22
rpoB 762263 c.2457C>T synonymous_variant 0.29
rpoC 765508 c.2139C>T synonymous_variant 0.15
rpoC 765628 c.2259G>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775901 p.Glu860Asp missense_variant 0.11
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781425 c.-135T>C upstream_gene_variant 0.11
rpsL 781714 p.Val52Ala missense_variant 0.1
fbiC 1303122 c.192G>T synonymous_variant 0.22
fbiC 1303159 p.Gly77Arg missense_variant 0.25
fbiC 1304224 p.Gly432Ser missense_variant 0.12
fbiC 1304662 p.Ser578Pro missense_variant 0.11
embR 1416355 c.993C>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471911 n.66C>T non_coding_transcript_exon_variant 0.18
rrs 1472116 n.271C>A non_coding_transcript_exon_variant 0.15
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 1.0
rrl 1476709 n.3052C>G non_coding_transcript_exon_variant 0.67
fabG1 1673728 p.Leu97Phe missense_variant 0.13
inhA 1674211 c.10C>T synonymous_variant 0.17
rpsA 1833955 c.414G>A synonymous_variant 0.12
rpsA 1834493 p.Glu318* stop_gained 0.13
tlyA 1917824 c.-116C>A upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 0.93
ndh 2102429 p.Asp205Val missense_variant 0.11
katG 2154490 p.Ala541Val missense_variant 0.12
katG 2155389 c.723C>G synonymous_variant 1.0
katG 2156139 c.-28G>T upstream_gene_variant 0.12
katG 2156293 c.-182C>T upstream_gene_variant 0.15
PPE35 2170385 c.228G>A synonymous_variant 0.18
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2222559 c.606G>A synonymous_variant 0.12
Rv1979c 2222941 p.Asn75Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714375 p.Val320Phe missense_variant 0.11
folC 2747650 c.-52G>A upstream_gene_variant 0.14
pepQ 2859616 p.Ala268Asp missense_variant 0.22
pepQ 2859883 p.Leu179Pro missense_variant 0.17
Rv2752c 3064637 p.Val519Leu missense_variant 0.13
Rv2752c 3066240 c.-49G>A upstream_gene_variant 0.25
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyX 3067481 c.465C>T synonymous_variant 0.18
thyX 3067717 c.228delC frameshift_variant 0.12
thyX 3067741 p.His69Asn missense_variant 0.1
thyX 3067874 c.72C>A synonymous_variant 0.12
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474420 c.414C>T synonymous_variant 0.14
fprA 3475132 p.Gln376Lys missense_variant 0.13
whiB7 3568617 c.63C>T synonymous_variant 0.11
Rv3236c 3612376 c.741A>G synonymous_variant 0.4
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
clpC1 4039719 p.Arg329His missense_variant 0.12
clpC1 4040687 c.18C>T synonymous_variant 0.11
clpC1 4040774 c.-70A>G upstream_gene_variant 0.13
embC 4239959 p.Ala33Thr missense_variant 0.12
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245343 p.Ser704Leu missense_variant 0.15
embB 4248423 p.Ala637Val missense_variant 0.15
embB 4248884 p.Asn791Tyr missense_variant 0.14
embB 4248967 c.2454G>A synonymous_variant 0.14
embB 4249011 p.Leu833Gln missense_variant 0.11
embB 4249647 p.Arg1045Gln missense_variant 0.12
embB 4249700 p.Ser1063Pro missense_variant 0.15
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4267709 c.1128C>T synonymous_variant 0.12
aftB 4267728 p.Trp370* stop_gained 0.14
aftB 4267985 c.852C>T synonymous_variant 0.15
aftB 4268323 p.Leu172Phe missense_variant 0.11
aftB 4268937 c.-101T>C upstream_gene_variant 0.18
ubiA 4269161 p.Ser225Pro missense_variant 0.14
ubiA 4269476 p.Leu120Val missense_variant 0.18
ubiA 4270011 c.-178A>T upstream_gene_variant 0.11
ethA 4326643 p.Asp277Glu missense_variant 0.15
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408019 p.Gly62Ser missense_variant 0.17