TB-Profiler result

Run: ERR2229076
Summary

Run ID: ERR2229076

Sample name:

Date: 31-03-2023 16:36:11

Number of reads: 490438

Percentage reads mapped: 99.4

Strain: lineage4

Drug-resistance: Other

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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
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
ethA 4326444 c.1029dupG frameshift_variant 0.33 ethionamide, ethionamide
ethA 4327294 p.Tyr60* stop_gained 0.15 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 7505 c.204C>T synonymous_variant 0.13
gyrA 8191 p.Ala297Asp missense_variant 0.14
fgd1 491677 p.Gln299* stop_gained 0.22
mshA 575260 c.-88A>G upstream_gene_variant 0.4
mshA 576108 p.Ala254Gly missense_variant 0.43
rpoB 760933 p.Gly376Asp missense_variant 0.13
rpoC 765253 c.1884C>T synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779193 p.Ser68Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302732 c.-199T>C upstream_gene_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304371 p.His481Asn missense_variant 0.33
rrs 1471652 n.-194G>T upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472656 n.814delG non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673335 c.-105C>A upstream_gene_variant 0.13
fabG1 1673346 c.-94C>G upstream_gene_variant 0.29
fabG1 1673349 c.-91G>C upstream_gene_variant 0.33
fabG1 1673380 c.-60C>G upstream_gene_variant 0.38
rpsA 1834316 p.Thr259Ser missense_variant 0.29
rpsA 1834979 p.Ser480Gly missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918159 p.Leu74Met missense_variant 0.29
ndh 2102859 p.Ile62Leu missense_variant 0.29
katG 2156208 c.-97A>G upstream_gene_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.56
PPE35 2170053 p.Thr187Ser missense_variant 0.5
PPE35 2170147 p.Ser156Ala missense_variant 0.12
PPE35 2170157 p.Ala152Ser missense_variant 0.13
Rv1979c 2222505 c.660T>C synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289453 c.-212G>T upstream_gene_variant 0.4
kasA 2518809 p.Lys232Arg missense_variant 0.5
Rv2752c 3065658 c.534G>A synonymous_variant 0.17
thyX 3067726 c.218_219delTA frameshift_variant 0.14
thyX 3067962 c.-17G>T upstream_gene_variant 0.25
thyA 3074520 c.-50_-49insC upstream_gene_variant 0.2
Rv3083 3448402 c.-102C>A upstream_gene_variant 0.25
fprA 3474890 p.Val295Ala missense_variant 0.2
fprA 3474892 p.Ser296Ala missense_variant 0.2
fbiB 3641868 p.Asn112His missense_variant 0.33
fbiB 3642099 p.Val189Phe missense_variant 0.13
fbiB 3642147 p.Val205Phe missense_variant 0.12
fbiB 3642153 p.Gly207Cys missense_variant 0.12
fbiB 3642615 p.Pro361Ser missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.14
clpC1 4039714 p.Tyr331His missense_variant 0.15
clpC1 4040057 c.648C>T synonymous_variant 0.33
embC 4240647 c.787delC frameshift_variant 0.17
embA 4242610 c.-623A>G upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248120 p.Ser536Leu missense_variant 0.13
embB 4248215 p.Arg568Ser missense_variant 0.25
embB 4248537 p.Leu675Gln missense_variant 0.22
ethR 4326961 c.-588G>C upstream_gene_variant 0.23
ethR 4326964 c.-585G>A upstream_gene_variant 0.21
ethR 4326970 c.-579G>T upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0