TB-Profiler result

Run: ERR4796798
Summary

Run ID: ERR4796798

Sample name:

Date: 01-04-2023 07:07:18

Number of reads: 6297901

Percentage reads mapped: 99.59

Strain: lineage4.1.1.3

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 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288650 c.524_*30delTGCGCACCGCCAGCGTCGAGTTGGTTTGCAGCTCCTGATGGCACCGCCGAACCGGGATGAACTGTTGG frameshift_variant&stop_lost&splice_region_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
thyA 3071917 c.-2233_*1762del transcript_ablation 1.0 para-aminosalicylic_acid
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 0.29
rpoB 759694 c.-113C>T upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
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
fabG1 1673553 p.Asp38Glu missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.21
thyX 3067949 c.-4C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.61
fbiD 3339744 c.627A>C synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.26
embC 4240409 p.Pro183Ala missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.13
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246563 p.Leu17Trp missense_variant 0.11
embB 4246567 c.54G>T synonymous_variant 0.15
embB 4249408 c.2895G>A synonymous_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407976 p.Gly76Asp missense_variant 1.0
pncA 2288650 c.523_*30delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC stop_lost&conservative_inframe_deletion&splice_region_variant 1.0