TB-Profiler result

Run: ERR3077938
Summary

Run ID: ERR3077938

Sample name:

Date: 01-04-2023 00:11:48

Number of reads: 816540

Percentage reads mapped: 99.48

Strain: lineage4.2.2.2

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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 761100 p.Gln432Glu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.19 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 5556 p.Gly106Ala missense_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
ccsA 620832 c.942C>A synonymous_variant 0.12
rpoB 761031 p.Gln409Glu missense_variant 0.1
rpoB 761248 p.Glu481Ala missense_variant 1.0
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoC 763711 c.342G>A synonymous_variant 0.14
mmpL5 775618 p.Pro955Thr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777317 c.1164C>A synonymous_variant 0.12
mmpL5 777435 p.Ala349Gly missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781822 p.Lys88Ile missense_variant 1.0
rpsL 781877 c.318T>C synonymous_variant 0.11
rplC 801338 p.Val177Ala missense_variant 0.1
fbiC 1304474 p.Leu515Pro missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918251 c.312T>C synonymous_variant 0.11
ndh 2101865 p.Trp393Ser missense_variant 0.15
ndh 2102520 p.Val175Phe missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288911 p.Glu111* stop_gained 1.0
eis 2714856 c.477T>A synonymous_variant 0.14
ribD 2987511 p.Arg225Ser missense_variant 0.13
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612214 c.903C>A synonymous_variant 0.12
Rv3236c 3612251 p.Ser289* stop_gained 0.2
Rv3236c 3612617 p.Pro167Leu missense_variant 0.12
rpoA 3878567 c.-60C>G upstream_gene_variant 0.14
ddn 3986956 p.Gly38Asp missense_variant 0.12
panD 4044414 c.-133G>T upstream_gene_variant 0.13
panD 4044453 c.-172G>T upstream_gene_variant 0.14
embC 4240830 p.Pro323His missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247387 p.Val292Leu missense_variant 0.1
aftB 4267926 p.Ala304Glu missense_variant 0.12
aftB 4268809 p.Val10Leu missense_variant 0.12
whiB6 4338403 p.Arg40Leu missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0