TB-Profiler result

Run: ERR11068799
Summary

Run ID: ERR11068799

Sample name:

Date: 07-04-2023 02:15:05

Number of reads: 2556024

Percentage reads mapped: 99.46

Strain: lineage4.2.2.1;lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 0.13
lineage4.2 Euro-American H;T;LAM None 0.88
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.86
lineage4.1.2 Euro-American T;H None 0.13
lineage4.2.2.1 Euro-American LAM7-TUR None 0.87
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.13
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 0.87 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.87 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.78 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 0.89 isoniazid, ethionamide
pncA 2288766 c.474_475dupCC frameshift_variant 0.89 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.88 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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.14
mshA 575679 p.Asn111Ser missense_variant 0.16
mshA 576077 c.730C>T synonymous_variant 0.88
rpoC 764959 c.1590G>A synonymous_variant 0.16
rpoC 765150 p.Gly594Glu missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 0.98
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 2102726 p.His106Arg missense_variant 0.74
Rv1979c 2223233 c.-69G>C upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.92
ald 3086742 c.-78A>C upstream_gene_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877956 p.Glu184Asp missense_variant 0.85
rpoA 3878572 c.-65G>C upstream_gene_variant 0.89
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.13
embB 4246584 p.Arg24Pro missense_variant 0.27
embB 4247024 p.Pro171Ala missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408009 p.Val65Ala missense_variant 0.91