TB-Profiler result

Run: SRR20139565
Summary

Run ID: SRR20139565

Sample name:

Date: 13-03-2023 09:19:32

Number of reads: 2617580

Percentage reads mapped: 99.62

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
pncA 2289105 p.Ala46Val missense_variant 0.45 pyrazinamide
pncA 2289132 c.107_108insCG frameshift_variant 0.48 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.21
fgd1 490756 c.-27T>G upstream_gene_variant 0.25
fgd1 490759 c.-24A>T upstream_gene_variant 0.15
fgd1 490780 c.-3C>A upstream_gene_variant 0.17
fgd1 490810 p.Ala10Thr missense_variant 0.15
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576744 p.Val466Gly missense_variant 0.15
rpoB 759615 c.-192A>C upstream_gene_variant 0.23
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781816 p.Arg86Gln missense_variant 1.0
fbiC 1303055 p.Asp42Gly missense_variant 0.19
fbiC 1304159 p.Val410Gly missense_variant 0.22
fbiC 1304166 c.1236A>G synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102814 p.Arg77Ser missense_variant 1.0
katG 2155687 p.Asp142Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726350 p.Trp53Leu missense_variant 0.26
ribD 2987323 p.Val162Gly missense_variant 0.16
thyA 3074601 c.-130T>G upstream_gene_variant 0.15
thyA 3074608 c.-137A>G upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
embC 4242387 p.Asn842Thr missense_variant 0.15
embC 4242393 p.Asp844Ala missense_variant 0.15
embA 4242406 c.-827A>C upstream_gene_variant 0.18
embA 4242442 c.-791G>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249305 p.Asn931Thr missense_variant 0.16
embB 4249323 p.Ala937Glu missense_variant 0.18
ubiA 4269742 p.Leu31Pro missense_variant 1.0
ethA 4327146 p.Ser110Pro missense_variant 1.0
ethR 4327803 p.Met85Ile missense_variant 1.0
ethA 4328212 c.-744_-743delCC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0