TB-Profiler result

Run: SRR6982214
Summary

Run ID: SRR6982214

Sample name:

Date: 04-04-2023 18:30:48

Number of reads: 605713

Percentage reads mapped: 99.09

Strain: lineage4.4.1.1

Drug-resistance: MDR-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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 0.99
lineage4.4.1.1 Euro-American S;Orphans None 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
gid 4407731 c.471delG 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 767123 p.Val1252Leu missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416428 p.Ala307Glu missense_variant 0.11
embR 1416733 p.Glu205Asp missense_variant 0.11
embR 1416833 p.Leu172Pro missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473854 n.197A>G non_coding_transcript_exon_variant 0.29
rrl 1473932 n.275C>A non_coding_transcript_exon_variant 0.22
rrl 1474014 n.357G>T non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155079 p.Lys345Glu missense_variant 0.1
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2169893 c.720C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064679 p.Glu505Lys missense_variant 0.11
thyX 3068074 c.-129C>A upstream_gene_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087017 c.198C>A synonymous_variant 0.11
fbiD 3339722 c.608_611delTAGG frameshift_variant 0.15
Rv3083 3448355 c.-149C>T upstream_gene_variant 0.11
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3612776 p.Asp114Val missense_variant 0.15
fbiB 3642693 p.Ala387Thr missense_variant 0.13
clpC1 4040524 p.Ser61Gly missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243917 c.689dupG frameshift_variant 0.15
embA 4245514 p.Asp761Gly missense_variant 0.14
embB 4246773 p.Val87Ala missense_variant 0.12
ethR 4327600 p.Ala18Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0