TB-Profiler result

Run: SRR7517727
Summary

Run ID: SRR7517727

Sample name:

Date: 04-04-2023 19:34:05

Number of reads: 1573285

Percentage reads mapped: 98.54

Strain: lineage4.2.2.2

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288933 p.Tyr103* stop_gained 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 5656 c.417C>A synonymous_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 760853 p.Met349Ile missense_variant 0.2
rpoB 761489 c.1683G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461161 c.117C>A synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.29
fabG1 1673478 p.Phe13Leu missense_variant 0.22
fabG1 1673668 p.Glu77* stop_gained 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102449 p.Lys198Asn missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715401 c.-69C>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448416 c.-88C>A upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640693 p.Ala51Ser missense_variant 0.17
rpoA 3877659 c.849G>T synonymous_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326120 p.Arg452Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0