TB-Profiler result

Run: SRR6480320
Summary

Run ID: SRR6480320

Sample name:

Date: 04-04-2023 14:33:06

Number of reads: 8516087

Percentage reads mapped: 99.7

Strain: lineage4.8

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
lineage4.8 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 761139 p.His445Asp missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 5787 p.Thr183Met missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460992 c.-53A>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102270 p.Thr258Ser missense_variant 1.0
katG 2155942 p.Pro57Leu missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288982 p.Thr87Met missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.2
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3878051 p.Arg153Trp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245605 c.-909G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448500 c.-3_*1407del transcript_ablation 1.0