TB-Profiler result

Run: ERR4813486
Summary

Run ID: ERR4813486

Sample name:

Date: 01-04-2023 12:47:07

Number of reads: 5920418

Percentage reads mapped: 99.61

Strain: lineage4

Drug-resistance: HR-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
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
gid 4407824 p.Gln127* stop_gained 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576602 p.Arg419Trp missense_variant 0.25
mshA 576621 p.Ala425Asp missense_variant 0.25
ccsA 619924 p.Arg12Cys missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779588 c.-683C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065926 p.Ala89Glu missense_variant 1.0
thyX 3067357 p.Ala197Ser missense_variant 0.29
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
embB 4247028 p.Leu172Arg missense_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0