TB-Profiler result

Run: ERR4812502

Summary

Run ID: ERR4812502

Sample name:

Date: 01-04-2023 12:07:06

Number of reads: 629778

Percentage reads mapped: 98.81

Strain: lineage4.1.2.1

Drug-resistance: Sensitive


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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
lineage4.1.2 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
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 8346 p.Val349Ile missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761675 c.1869G>T synonymous_variant 0.12
rpoC 763362 c.-8G>A upstream_gene_variant 0.2
rpoC 763582 p.Lys71Asn missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766706 p.Glu1113* stop_gained 0.38
rpoC 767108 p.Gly1247Ser missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801311 p.Gly168Glu missense_variant 0.15
fbiC 1303289 p.Ser120Asn missense_variant 0.17
fbiC 1305438 c.2508C>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475730 n.2073G>T non_coding_transcript_exon_variant 0.25
rpsA 1833600 p.Glu20Gly missense_variant 0.18
rpsA 1833940 c.399C>A synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918218 c.279C>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714867 p.Gly156Ser missense_variant 0.12
eis 2715390 c.-58C>T upstream_gene_variant 0.11
ahpC 2725982 c.-211G>A upstream_gene_variant 0.12
ahpC 2726691 c.502delC frameshift_variant 0.18
thyX 3068152 c.-208_-207insG upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612241 c.876G>T synonymous_variant 0.12
rpoA 3878623 c.-116C>A upstream_gene_variant 0.33
clpC1 4039551 p.Leu385Pro missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244294 c.1062G>T synonymous_variant 0.13
aftB 4267089 p.Thr583Ser missense_variant 0.11
aftB 4267917 p.Ser307Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0