TB-Profiler result

Run: SRR9224986
Summary

Run ID: SRR9224986

Sample name:

Date: 04-04-2023 22:09:00

Number of reads: 790031

Percentage reads mapped: 89.04

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;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
rpoB 761098 p.Ser431Thr missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
ethR 4327876 p.Phe110Leu missense_variant 1.0 ethionamide
gid 4407851 c.351delG frameshift_variant 1.0 streptomycin
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 5866 c.627C>T synonymous_variant 0.11
gyrB 6609 p.Val457Ala missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
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
mmpL5 776568 p.Met638Lys missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 1.0
embR 1417133 p.Ile72Thr missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472406 n.561G>T non_coding_transcript_exon_variant 0.11
rrl 1476417 n.2760T>C non_coding_transcript_exon_variant 1.0
rpsA 1834291 p.Glu250Asp missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102578 c.465C>T synonymous_variant 0.11
PPE35 2168303 c.2310G>T synonymous_variant 1.0
Rv1979c 2222472 c.693A>G synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T 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 3613023 p.Pro32Ser missense_variant 1.0
alr 3840263 c.1158C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4326920 p.Ala185Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0