TB-Profiler result

Run: ERR2229737
Summary

Run ID: ERR2229737

Sample name:

Date: 31-03-2023 17:30:04

Number of reads: 566953

Percentage reads mapped: 99.2

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
katG 2155532 c.579delC frameshift_variant 0.2 isoniazid
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 8406 p.Gln369* stop_gained 0.12
mshA 575256 c.-92C>T upstream_gene_variant 0.13
mshA 575418 p.Ala24Asp missense_variant 0.2
ccsA 619880 c.-11A>T upstream_gene_variant 0.2
rpoB 760294 p.Asn163Ile missense_variant 0.14
rpoB 760979 p.Glu391Asp missense_variant 0.22
rpoC 764840 p.Ile491Val missense_variant 0.11
rpoC 765761 p.Pro798Ala missense_variant 0.2
rpoC 765922 c.2553C>T synonymous_variant 0.38
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778405 p.Arg26Gly missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304140 p.Ala404Ser missense_variant 0.25
fbiC 1304399 p.Arg490His missense_variant 0.13
embR 1417481 c.-134G>T upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472280 n.435C>G non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
fabG1 1673771 p.Ala111Asp missense_variant 0.22
inhA 1674253 p.Asp18Asn missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918540 p.Pro201Thr missense_variant 0.17
ndh 2103174 c.-132G>T upstream_gene_variant 0.17
katG 2154117 c.1995T>G synonymous_variant 0.12
katG 2154620 p.Arg498Ser missense_variant 0.14
katG 2155506 c.606C>T synonymous_variant 0.14
PPE35 2167742 c.2871C>A synonymous_variant 0.5
PPE35 2167865 c.2748G>C synonymous_variant 0.18
PPE35 2167868 c.2745A>C synonymous_variant 0.18
PPE35 2168687 c.1926C>A synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168888 c.1725G>T synonymous_variant 0.22
PPE35 2169269 c.1344A>G synonymous_variant 0.19
PPE35 2169272 c.1341C>G synonymous_variant 0.18
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.13
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169293 c.1320T>C synonymous_variant 0.13
PPE35 2169308 c.1305C>T synonymous_variant 0.12
PPE35 2169890 c.723C>T synonymous_variant 0.15
PPE35 2169893 c.720C>A synonymous_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.53
PPE35 2170066 p.Ala183Thr missense_variant 0.25
PPE35 2170155 p.Ala153Gly missense_variant 0.3
PPE35 2170157 c.456G>C synonymous_variant 0.3
PPE35 2170319 p.Glu98Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289258 c.-17G>T upstream_gene_variant 0.12
eis 2715267 c.66C>A synonymous_variant 0.12
eis 2715427 c.-95T>C upstream_gene_variant 0.25
folC 2746374 p.Pro409Ala missense_variant 0.22
pepQ 2860359 c.60T>C synonymous_variant 0.14
Rv2752c 3064901 p.Leu431Val missense_variant 0.29
Rv2752c 3064906 p.Val429Ala missense_variant 0.25
Rv2752c 3066126 c.66C>A synonymous_variant 0.12
thyX 3067953 c.-8T>C upstream_gene_variant 0.12
thyA 3074659 c.-188G>A upstream_gene_variant 0.13
fprA 3474199 p.Lys65Glu missense_variant 0.17
fprA 3474840 c.834C>A synonymous_variant 0.22
fbiA 3640813 p.Glu91Gln missense_variant 0.1
alr 3840844 c.576delG frameshift_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.17
rpoA 3877730 p.Ser260Ala missense_variant 0.14
clpC1 4038829 p.Glu626Gln missense_variant 0.12
clpC1 4039654 p.Thr351Ser missense_variant 0.15
panD 4044371 c.-90G>T upstream_gene_variant 0.13
embC 4240466 p.Thr202Ala missense_variant 0.12
embC 4240769 p.Val303Met missense_variant 0.12
embC 4242063 p.Trp734Leu missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244371 p.Arg380His missense_variant 0.2
embB 4249140 p.Val876Glu missense_variant 0.19
aftB 4268146 p.Tyr231His missense_variant 0.12
ethR 4327018 c.-531G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407936 c.267T>A synonymous_variant 0.15
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0