TB-Profiler result

Run: SRR14782320
Summary

Run ID: SRR14782320

Sample name:

Date: 03-04-2023 11:20:45

Number of reads: 1460401

Percentage reads mapped: 99.39

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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 7564 p.Gly88Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
rpoB 761284 p.Ser493Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
pncA 2288821 p.Gln141* stop_gained 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.98 kanamycin
embB 4247429 p.Met306Val 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.98
gyrA 9647 c.2346C>G synonymous_variant 0.19
fgd1 491247 c.465C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.12
ccsA 619969 p.Val27Ile missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.26
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.24
inhA 1673556 c.-646C>G upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.22
pepQ 2860159 p.Ala87Gly missense_variant 0.15
ald 3086742 c.-78A>C upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fbiD 3339734 p.Ala206Gly missense_variant 0.62
fbiD 3339751 p.Ala212Pro missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.67
whiB7 3568428 c.252A>C synonymous_variant 0.6
whiB7 3568431 c.249C>G synonymous_variant 0.22
alr 3840463 p.Arg320Trp missense_variant 0.96
rpoA 3878551 c.-44C>A upstream_gene_variant 0.11
rpoA 3878641 c.-134C>G upstream_gene_variant 0.75
embC 4240409 p.Pro183Ala missense_variant 0.44
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.33
embB 4248328 c.1815G>C synonymous_variant 0.26
embB 4249594 c.3081G>A synonymous_variant 0.98
ethA 4326632 p.His281Pro missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0