TB-Profiler result

Run: SRR16088142
Summary

Run ID: SRR16088142

Sample name:

Date: 03-04-2023 16:04:16

Number of reads: 4387420

Percentage reads mapped: 99.51

Strain: lineage4.2.1

Drug-resistance: HR-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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.24
mshA 576108 p.Ala254Gly missense_variant 0.29
mshA 576113 p.Arg256Gly missense_variant 0.23
mshA 576616 c.1269G>C synonymous_variant 0.22
rpoC 764367 p.Gly333Ala missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.19
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 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.17
PPE35 2169879 p.Phe245Cys missense_variant 0.99
PPE35 2170065 p.Ala183Gly missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517966 c.-149G>A upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.22
pepQ 2860159 p.Ala87Gly missense_variant 0.12
Rv2752c 3064823 p.Val457Leu missense_variant 0.19
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.54
fbiD 3339749 p.Val211Gly missense_variant 0.25
fbiD 3339751 p.Ala212Pro missense_variant 0.34
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474213 p.Lys69Asn missense_variant 0.17
whiB7 3568428 c.252A>G synonymous_variant 0.42
whiB7 3568431 c.249C>G synonymous_variant 0.28
rpoA 3878590 c.-83G>C upstream_gene_variant 0.18
rpoA 3878597 c.-90G>C upstream_gene_variant 0.5
rpoA 3878641 c.-134C>G upstream_gene_variant 0.63
embC 4240409 p.Pro183Ala missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.33
embB 4248328 c.1815G>C synonymous_variant 0.26
embB 4249594 c.3081G>A synonymous_variant 1.0
aftB 4268137 c.700C>T synonymous_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338205 p.Val106Gly missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0