TB-Profiler result

Run: SRR6896556
Summary

Run ID: SRR6896556

Sample name:

Date: 04-04-2023 18:09:43

Number of reads: 207165

Percentage reads mapped: 99.52

Strain: lineage4.3.2.1

Drug-resistance: Other

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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
lineage4.3.2 Euro-American (LAM) LAM3 None 0.98
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
ethA 4327176 c.297dupG frameshift_variant 0.17 ethionamide
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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619785 c.-106G>A upstream_gene_variant 0.14
rpoB 760433 p.Asp209Glu missense_variant 0.25
rpoB 761476 p.Arg557His missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303569 p.Met213Ile missense_variant 0.17
embR 1416620 p.Pro243His missense_variant 0.14
atpE 1461276 p.Thr78Ala missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475063 n.1406A>G non_coding_transcript_exon_variant 0.14
rpsA 1834944 p.Ala468Val missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167937 c.2676A>G synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518088 c.-27T>C upstream_gene_variant 0.2
kasA 2518151 p.Ser13Arg missense_variant 0.2
eis 2715078 c.255C>G synonymous_variant 0.22
thyX 3067552 c.352_393delGTGCCGCCCGGCATGGAGGACGACGCCGACCTGCGCCACATC conservative_inframe_deletion 0.2
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074080 p.Ser131Leu missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087259 p.Tyr147Cys missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474791 p.Pro262Gln missense_variant 0.14
fbiB 3640866 c.-669T>C upstream_gene_variant 0.18
fbiB 3641717 c.183T>C synonymous_variant 0.15
alr 3841199 c.222T>C synonymous_variant 0.13
alr 3841538 c.-118T>C upstream_gene_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039538 c.1167C>T synonymous_variant 0.13
embC 4242339 p.Thr826Asn missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248201 p.Ile563Asn missense_variant 0.15
embB 4248409 c.1896A>G synonymous_variant 0.25
aftB 4267934 c.903G>A synonymous_variant 1.0
aftB 4268276 c.561G>A synonymous_variant 0.22
ubiA 4269679 p.Leu52His missense_variant 0.18
ethA 4326295 c.1179G>A synonymous_variant 1.0
whiB6 4338354 c.168C>T synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0