TB-Profiler result

Run: SRR22528544
Summary

Run ID: SRR22528544

Sample name:

Date: 04-04-2023 04:18:25

Number of reads: 1786271

Percentage reads mapped: 99.75

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8116 p.Thr272Ile missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576123 p.Leu259Arg missense_variant 0.12
rpoB 761528 p.Asp574Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472762 n.922delG non_coding_transcript_exon_variant 0.17
rrs 1473023 n.1178G>A non_coding_transcript_exon_variant 0.13
rrl 1476391 n.2734C>T non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074495 c.-24C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3878569 c.-62C>T upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embA 4244970 c.1738C>T synonymous_variant 1.0
embB 4246582 c.69T>G synonymous_variant 0.11
embB 4248437 p.Thr642Ala missense_variant 1.0
ethR 4326703 c.-846T>C upstream_gene_variant 1.0
whiB6 4338514 p.Tyr3Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0