TB-Profiler result

Run: SRR6896550
Summary

Run ID: SRR6896550

Sample name:

Date: 04-04-2023 18:09:35

Number of reads: 676758

Percentage reads mapped: 98.26

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 0.98
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.97
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 761108 p.Met434Ile missense_variant 0.17 rifampicin
katG 2155703 c.408delC frameshift_variant 0.15 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
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 6581 p.Thr448Ala missense_variant 0.1
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491443 p.Ser221Pro missense_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775934 p.Asp849Glu missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461077 c.33C>T synonymous_variant 0.14
atpE 1461123 p.Gly27Arg missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471834 n.-12G>T upstream_gene_variant 0.12
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473980 n.325dupG non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155096 p.Tyr339Cys missense_variant 0.11
PPE35 2168354 c.2259G>T synonymous_variant 0.11
PPE35 2168457 p.Val719Ala missense_variant 0.15
PPE35 2169310 p.Gly435Arg missense_variant 0.11
PPE35 2169691 c.921delC frameshift_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714552 p.Ser261Pro missense_variant 0.1
pepQ 2859372 c.1047G>A synonymous_variant 0.13
pepQ 2859750 c.669C>A synonymous_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086901 p.Arg28Cys missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568650 c.30C>A synonymous_variant 0.88
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038963 p.Asp581Val missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0