TB-Profiler result

Run: ERR2653124
Summary

Run ID: ERR2653124

Sample name:

Date: 31-03-2023 22:33:13

Number of reads: 6807049

Percentage reads mapped: 97.26

Strain: lineage4.1.1

Drug-resistance: Pre-XDR-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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
gyrA 7570 p.Ala90Val missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.78 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.99 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Ala missense_variant 0.98 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.99 ethambutol
gid 4408100 c.102delG 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 9304 p.Gly668Asp missense_variant 1.0
rpoB 762027 p.Leu741Phe missense_variant 1.0
rpoB 762310 p.His835Pro missense_variant 0.99
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765730 c.2361G>A synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781767 p.Glu70Lys missense_variant 0.98
rplC 801115 p.Ala103Thr missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167931 c.2682C>T synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 1.0
Rv2752c 3065707 c.484delG frameshift_variant 0.78
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 0.99
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3878565 c.-60C>G upstream_gene_variant 0.11
rpoA 3878599 c.-92C>G upstream_gene_variant 0.12
rpoA 3878601 c.-95delG upstream_gene_variant 0.18
embC 4240897 c.1035C>G synonymous_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 0.99
ethA 4327331 p.Phe48Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0