TB-Profiler result

Run: ERR2229748
Summary

Run ID: ERR2229748

Sample name:

Date: 31-03-2023 17:33:05

Number of reads: 554355

Percentage reads mapped: 99.22

Strain: lineage4

Drug-resistance: RR-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
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
rpoC 764948 p.Leu527Val missense_variant 0.18 rifampicin
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
fgd1 491737 p.Arg319Trp missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoB 762247 p.Leu814Pro missense_variant 0.29
rpoC 763382 p.Asn5Asp missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304395 p.Glu489Lys missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474084 n.431delA non_coding_transcript_exon_variant 0.17
rrl 1474242 n.585A>G non_coding_transcript_exon_variant 0.22
rrl 1476755 n.3098G>T non_coding_transcript_exon_variant 0.2
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.64
rpsA 1833392 c.-150C>A upstream_gene_variant 0.2
rpsA 1834113 c.574dupG frameshift_variant 0.22
rpsA 1834173 p.Ile211Thr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101918 p.Arg375Ser missense_variant 0.12
ndh 2102909 p.Arg45His missense_variant 0.22
katG 2154646 p.Arg489His missense_variant 0.18
katG 2154994 p.Arg373Leu missense_variant 0.2
katG 2156242 c.-131C>T upstream_gene_variant 0.13
PPE35 2167847 c.2766A>C synonymous_variant 0.29
PPE35 2167865 c.2748G>C synonymous_variant 0.4
PPE35 2167868 c.2745A>C synonymous_variant 0.5
PPE35 2167878 p.Ser912Asn missense_variant 0.25
PPE35 2168047 p.Leu856Val missense_variant 0.29
PPE35 2168051 p.Val854Ile missense_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.12
PPE35 2169272 c.1341C>G synonymous_variant 0.12
PPE35 2169278 c.1335T>C synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.14
PPE35 2169840 p.Gly258Asp missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.88
PPE35 2170053 p.Thr187Ser missense_variant 0.88
PPE35 2170262 c.351C>G synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519153 p.Ile347Val missense_variant 0.25
eis 2715266 p.Ser23Gly missense_variant 0.15
thyX 3067340 c.606G>A synonymous_variant 0.29
ald 3086862 c.43C>A synonymous_variant 0.17
fprA 3474513 c.507T>C synonymous_variant 0.17
fprA 3475187 p.Glu394Gly missense_variant 0.18
fbiA 3640508 c.-35T>C upstream_gene_variant 0.22
alr 3840403 c.1017delG frameshift_variant 0.5
alr 3840553 p.Gly290Arg missense_variant 0.18
clpC1 4038293 c.2412G>A synonymous_variant 0.25
clpC1 4038752 p.Gln651His missense_variant 0.18
clpC1 4039100 c.1605C>A synonymous_variant 0.14
clpC1 4039829 p.Leu292Ile missense_variant 0.25
embC 4239963 p.Val34Ala missense_variant 0.15
embC 4240915 p.Met351Ile missense_variant 0.15
embC 4242140 p.Asp760Tyr missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246321 p.Phe1030Ser missense_variant 0.11
embA 4246353 p.Thr1041Ala missense_variant 0.11
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4247470 c.957T>C synonymous_variant 0.15
embB 4247472 p.Phe320Tyr missense_variant 0.15
embB 4248496 c.1983G>A synonymous_variant 0.25
aftB 4267880 c.957C>T synonymous_variant 0.4
ethA 4326614 p.Asn287Thr missense_variant 0.14
ethA 4327869 c.-396G>T upstream_gene_variant 0.12
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0