TB-Profiler result

Run: SRR6797812
Summary

Run ID: SRR6797812

Sample name:

Date: 04-04-2023 16:18:56

Number of reads: 3730661

Percentage reads mapped: 99.53

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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247574 p.Asp354Ala missense_variant 0.98 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
rpoC 762680 c.-690C>T upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Leu missense_variant 0.99
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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288772 p.Val157Gly missense_variant 0.86
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244134 p.Glu301Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407979 p.Pro75Leu missense_variant 1.0
pncA 2285034 c.469_*3646del stop_lost&conservative_inframe_deletion&splice_region_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0