TB-Profiler result

Run: SRR14802126
Summary

Run ID: SRR14802126

Sample name:

Date: 03-04-2023 12:16:43

Number of reads: 3537983

Percentage reads mapped: 99.41

Strain: lineage4.1

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
lineage4.1 Euro-American T;X;H 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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Gly missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4407627 c.574_575delGG 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7374 p.Gln25Glu missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
mshA 576613 c.1266A>C synonymous_variant 0.25
mshA 576616 c.1269G>C synonymous_variant 0.12
mshA 576719 p.Glu458Gln missense_variant 1.0
rpoC 764819 p.Trp484Gly missense_variant 1.0
rpoC 765150 p.Gly594Glu 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
rrs 1471745 n.-101_-100insG upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154634 p.Asn493Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.37
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747160 p.Pro147Ser missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.43
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878637 c.-130G>C upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 0.48
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.22
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269295 p.Met180Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0