TB-Profiler result

Run: SRR15368792
Summary

Run ID: SRR15368792

Sample name:

Date: 03-04-2023 13:49:52

Number of reads: 7093551

Percentage reads mapped: 99.39

Strain: lineage4.4.2

Drug-resistance: Pre-XDR-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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 None 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
gyrA 7582 p.Asp94Ala missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760663 p.Ala286Val missense_variant 1.0 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala 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 5077 c.-163_-162insC 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
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169041 c.1572G>A synonymous_variant 0.39
PPE35 2169044 c.1569G>C synonymous_variant 0.44
PPE35 2169047 p.Ile522Val missense_variant 0.37
PPE35 2169053 c.1560T>C synonymous_variant 0.96
PPE35 2169056 c.1557A>G synonymous_variant 0.37
PPE35 2169059 c.1554G>A synonymous_variant 0.59
PPE35 2169063 p.Met517Thr missense_variant 0.96
PPE35 2169065 p.Ala516Ile missense_variant 0.59
PPE35 2169068 c.1545G>T synonymous_variant 0.62
PPE35 2169071 c.1542A>G synonymous_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860189 p.Arg77His missense_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877969 p.Ala180Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.99
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338389 p.Pro45Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408118 p.Pro29Thr missense_variant 1.0