TB-Profiler result

Run: ERR3323731
Summary

Run ID: ERR3323731

Sample name:

Date: 01-04-2023 01:49:10

Number of reads: 5151890

Percentage reads mapped: 99.67

Strain: lineage4.4.1.1;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 0.14
lineage4.4 Euro-American S;T None 0.87
lineage4.4.1 Euro-American (S-type) S;T None 0.87
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.14
lineage4.4.1.1 Euro-American S;Orphans None 0.86
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 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 0.16 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.11 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.14 isoniazid, ethionamide
tlyA 1918415 p.Ser159* stop_gained 0.16 capreomycin
katG 2155168 p.Ser315Thr missense_variant 0.13 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.16 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.1 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
mshA 576108 p.Ala254Gly missense_variant 0.21
mshA 576482 p.Val379Leu missense_variant 0.12
ccsA 619969 p.Val27Ile missense_variant 0.15
rpoB 762391 p.Leu862Arg missense_variant 0.15
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.91
PPE35 2169840 p.Gly258Asp missense_variant 0.87
PPE35 2169879 p.Phe245Cys missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519198 c.1084C>T synonymous_variant 0.84
thyA 3074093 p.Arg127Cys missense_variant 0.91
ald 3086742 c.-78A>C upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.34
Rv3083 3448608 c.105G>A synonymous_variant 0.86
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.92
rpoA 3878637 c.-130G>C upstream_gene_variant 0.23
rpoA 3878641 c.-134C>G upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.48
embB 4249594 c.3081G>A synonymous_variant 0.14
ethA 4326632 p.His281Pro missense_variant 0.14
ethA 4328376 c.-903G>C upstream_gene_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0