TB-Profiler result

Run: SRR4034388
Summary

Run ID: SRR4034388

Sample name:

Date: 04-04-2023 06:45:52

Number of reads: 1929706

Percentage reads mapped: 98.16

Strain: 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 0.99
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 761139 p.His445Tyr missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289031 p.His71Tyr missense_variant 1.0 pyrazinamide
ald 3086951 c.133delA frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247728 p.Glu405Asp missense_variant 1.0 ethambutol
gid 4407802 p.Ala134Glu missense_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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 619805 c.-86C>T upstream_gene_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765101 c.1732C>A synonymous_variant 0.11
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
Rv1258c 1406813 c.528T>C synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472470 n.625C>T non_coding_transcript_exon_variant 0.12
rrl 1475017 n.1360G>A non_coding_transcript_exon_variant 0.33
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.11
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.1
rpsA 1833382 c.-160G>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288776 c.466C>T synonymous_variant 0.17
pncA 2288784 p.Thr153Ile missense_variant 0.17
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518959 p.Ala282Asp missense_variant 0.12
eis 2715029 p.Ala102Thr missense_variant 0.29
folC 2747348 p.Ala84Val missense_variant 0.18
ribD 2986720 c.-119C>A upstream_gene_variant 0.12
ribD 2987168 c.330C>A synonymous_variant 0.14
Rv2752c 3064537 p.Val552Ala missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
alr 3840259 p.Tyr388Asp missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.13
embC 4240280 p.Val140Ile missense_variant 0.13
embC 4241487 p.Leu542Pro missense_variant 0.12
embC 4242190 c.2328C>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247738 p.Ala409Pro missense_variant 1.0
embB 4247975 p.Val488Ile missense_variant 0.11
ethA 4326842 p.Tyr211Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0