TB-Profiler result

Run: ERR2229235
Summary

Run ID: ERR2229235

Sample name:

Date: 31-03-2023 16:50:40

Number of reads: 455083

Percentage reads mapped: 99.15

Strain: lineage4.8

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
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
rpoB 761144 p.Lys446Asn missense_variant 0.22 rifampicin
pncA 2289099 p.Lys48Thr missense_variant 0.29 pyrazinamide
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 8064 p.Gly255Arg missense_variant 0.14
gyrA 8952 p.Gln551Lys missense_variant 0.14
fgd1 491021 p.Arg80His missense_variant 0.12
rpoB 761048 c.1242C>A synonymous_variant 0.22
rpoB 761915 p.Asp703Glu missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.2
mmpL5 777122 c.1359C>T synonymous_variant 0.2
mmpL5 777128 c.1353A>G synonymous_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473612 n.-46A>G upstream_gene_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1674732 c.531C>T synonymous_variant 0.29
rpsA 1833464 c.-78A>G upstream_gene_variant 0.2
tlyA 1917862 c.-78G>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102345 p.Ala233Asp missense_variant 0.2
ndh 2102625 p.Ser140Thr missense_variant 0.2
ndh 2102632 c.411C>A synonymous_variant 0.2
katG 2154170 p.Glu648Lys missense_variant 0.15
katG 2155286 p.His276Asn missense_variant 0.22
PPE35 2167746 p.Thr956Ile missense_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.15
PPE35 2168383 p.Phe744Ile missense_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168807 c.1806C>T synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.11
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169378 p.Phe412Tyr missense_variant 0.14
PPE35 2169717 p.Asn299Ile missense_variant 0.18
PPE35 2169732 p.Asn294Ser missense_variant 0.18
PPE35 2169868 p.Ser249Pro missense_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.25
PPE35 2169910 p.Asn235Tyr missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289898 c.-657C>A upstream_gene_variant 0.29
kasA 2519140 c.1026G>C synonymous_variant 0.38
kasA 2519143 c.1029G>C synonymous_variant 0.38
kasA 2519225 p.Leu371Met missense_variant 0.22
eis 2714309 p.Pro342Ser missense_variant 0.14
ribD 2987435 c.600delG frameshift_variant 0.2
thyX 3067806 p.Trp47Ser missense_variant 0.18
thyA 3074136 c.336C>A synonymous_variant 0.25
thyA 3074173 p.Ser100Leu missense_variant 0.22
ald 3087237 p.Leu140Ile missense_variant 0.2
fprA 3474143 p.Trp46Tyr missense_variant 0.15
fprA 3474165 c.159C>G synonymous_variant 0.2
alr 3840517 p.Pro302Thr missense_variant 0.18
alr 3841019 c.402G>A synonymous_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.24
clpC1 4038651 p.Gly685Val missense_variant 0.25
embC 4240848 p.Asp329Gly missense_variant 0.12
embC 4241367 p.Leu502His missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246260 p.Asp1010Tyr missense_variant 0.29
embB 4246527 p.Ala5Glu missense_variant 0.4
embB 4246567 c.54_55insT frameshift_variant 0.25
embB 4246591 c.78G>A synonymous_variant 0.15
embB 4249064 p.Gly851Cys missense_variant 0.22
aftB 4268217 p.Trp207* stop_gained 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0