TB-Profiler result

Run: SRR6785525

Summary

Run ID: SRR6785525

Sample name:

Date: 04-04-2023 16:01:42

Number of reads: 1136054

Percentage reads mapped: 99.62

Strain: lineage4.8

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
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 8039 c.738T>A synonymous_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.11
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
fabG1 1673380 c.-60C>G upstream_gene_variant 0.32
rpsA 1834113 p.Leu191Gln missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169717 p.Asn299Ile missense_variant 0.12
PPE35 2169719 c.894C>T synonymous_variant 0.12
PPE35 2169725 c.888T>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170157 p.Ala152Ser missense_variant 0.17
PPE35 2170238 c.375T>G synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746136 c.1463G>A splice_region_variant&stop_retained_variant 1.0
folC 2747083 c.516G>C synonymous_variant 0.15
Rv2752c 3064988 p.Met402Val missense_variant 0.1
fbiB 3642829 p.Pro432Gln missense_variant 0.14
alr 3840845 c.576G>T synonymous_variant 1.0
rpoA 3878490 c.18C>G synonymous_variant 0.25
clpC1 4038752 p.Gln651His missense_variant 0.12
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040605 p.Leu34Ile missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326059 p.Lys472Met missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407823 p.Gln127Leu missense_variant 0.18
gid 4408070 p.Trp45Arg missense_variant 1.0
Rv3083 3448450 c.-53_*1408del transcript_ablation 1.0