TB-Profiler result

Run: SRR16149168
Summary

Run ID: SRR16149168

Sample name:

Date: 03-04-2023 16:30:18

Number of reads: 2038081

Percentage reads mapped: 99.39

Strain: lineage4.2.2.1

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
lineage4.2.2.1 Euro-American 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2289036 p.Pro69Leu missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472578 n.733G>T non_coding_transcript_exon_variant 0.25
rrl 1474864 n.1207C>G non_coding_transcript_exon_variant 0.33
rrl 1475128 n.1471T>C non_coding_transcript_exon_variant 0.22
rrl 1475137 n.1480A>T non_coding_transcript_exon_variant 0.22
rrl 1475827 n.2170A>G non_coding_transcript_exon_variant 0.67
rrl 1475863 n.2206G>A non_coding_transcript_exon_variant 0.2
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.18
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.18
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.18
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.18
rrl 1475935 n.2278T>C non_coding_transcript_exon_variant 0.18
rrl 1476442 n.2788delG non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102726 p.His106Arg missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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
rpoA 3877956 p.Glu184Asp missense_variant 1.0
rpoA 3878572 c.-65G>C upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408009 p.Val65Ala missense_variant 1.0