TB-Profiler result

Run: ERR2503450
Summary

Run ID: ERR2503450

Sample name:

Date: 31-03-2023 18:28:02

Number of reads: 445988

Percentage reads mapped: 99.59

Strain: lineage4.5

Drug-resistance: HR-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
lineage4.5 Euro-American H;T RD122 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407851 c.351delG 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
gyrB 6094 c.855C>T synonymous_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
embR 1416528 p.Val274Phe missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472730 n.885A>G non_coding_transcript_exon_variant 0.17
rrl 1475378 n.1721A>G non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289888 c.-647G>A upstream_gene_variant 0.2
pncA 2290104 c.-863G>A upstream_gene_variant 0.22
eis 2714411 p.Arg308Cys missense_variant 0.11
Rv2752c 3064799 c.1391_1392delAG frameshift_variant 0.25
thyX 3067708 p.Phe80Leu missense_variant 0.11
Rv3083 3448675 p.Asp58His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474588 c.582G>C synonymous_variant 1.0
Rv3236c 3612306 p.Ala271Thr missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 1.0
alr 3841568 c.-148G>A upstream_gene_variant 1.0
alr 3841570 c.-151delA upstream_gene_variant 1.0
alr 3841574 c.-154T>G upstream_gene_variant 1.0
alr 3841578 c.-158G>T upstream_gene_variant 1.0
alr 3841582 c.-162A>G upstream_gene_variant 1.0
alr 3841584 c.-164C>A upstream_gene_variant 1.0
alr 3841589 c.-170delG upstream_gene_variant 1.0
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
clpC1 4039745 c.960C>T synonymous_variant 1.0
embC 4241764 c.1902C>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242984 p.Arg1041His missense_variant 0.14
aftB 4268802 p.Ala12Val missense_variant 0.14
ethA 4326005 c.1469A>G stop_lost&splice_region_variant 0.12
ethA 4327205 p.Ala90Val missense_variant 1.0
whiB6 4338594 c.-73T>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408398 c.-196C>G upstream_gene_variant 1.0