TB-Profiler result

Run: SRR11567800
Summary

Run ID: SRR11567800

Sample name:

Date: 02-04-2023 21:43:11

Number of reads: 9972505

Percentage reads mapped: 99.34

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 0.99
lineage4.4.2 Euro-American T1;T2 None 0.99
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 7570 p.Ala90Val missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.99 rifampicin
rpoB 761109 p.Asp435Asn missense_variant 0.99 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.96 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289103 p.Thr47Pro missense_variant 0.98 pyrazinamide
embB 4248003 p.Gln497Pro 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
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
Rv1258c 1407069 c.271delC frameshift_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102497 c.546T>C synonymous_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613282 c.-166G>A upstream_gene_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.99
embB 4248441 p.Thr643Ile missense_variant 0.98
aftB 4268928 c.-92C>T upstream_gene_variant 0.97
aftB 4269375 c.-539G>A upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407863 c.339dupG frameshift_variant 0.13