TB-Profiler result

Run: SRR6484839
Summary

Run ID: SRR6484839

Sample name:

Date: 04-04-2023 14:48:05

Number of reads: 1323451

Percentage reads mapped: 99.69

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 0.99
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
katG 2155149 p.Trp321Cys missense_variant 0.18 isoniazid
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 576108 p.Ala254Gly missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461028 c.-17T>A upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473659 n.2T>C non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475473 n.1816A>G non_coding_transcript_exon_variant 0.29
rrl 1475825 n.2168G>T non_coding_transcript_exon_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918064 p.Pro42Arg missense_variant 0.14
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.28
PPE35 2170053 p.Thr187Ser missense_variant 0.29
PPE35 2170518 p.Asp32Thr missense_variant 0.1
PPE35 2170540 c.73C>T synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289875 c.-634C>T upstream_gene_variant 0.14
fbiD 3339734 p.Ala206Gly missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244356 p.Phe375Ser missense_variant 0.12
embA 4244414 c.1182G>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0