TB-Profiler result

Run: SRR6485146
Summary

Run ID: SRR6485146

Sample name:

Date: 04-04-2023 15:11:21

Number of reads: 2122252

Percentage reads mapped: 99.76

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 761161 p.Leu452Pro missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289091 p.His51Asp missense_variant 1.0 pyrazinamide
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
gyrB 6084 p.Gly282Asp missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575378 p.Gly11Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779426 p.Met146Arg missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461045 c.1A>T initiator_codon_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476546 n.2889C>A non_coding_transcript_exon_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155654 p.Lys153Arg missense_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169185 c.1428C>T synonymous_variant 0.2
PPE35 2169191 c.1422G>C synonymous_variant 0.18
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.48
PPE35 2170053 p.Thr187Ser missense_variant 0.5
PPE35 2170147 p.Ser156Ala missense_variant 0.14
PPE35 2170157 p.Ala152Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3236c 3612560 p.Thr186Met missense_variant 1.0
Rv3236c 3613035 p.Phe28Leu missense_variant 1.0
rpoA 3878490 c.18C>G synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245825 p.Asp865Asn missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407917 p.Arg96Cys missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0