TB-Profiler result

Run: ERR972799
Summary

Run ID: ERR972799

Sample name:

Date: 02-04-2023 12:02:56

Number of reads: 6765032

Percentage reads mapped: 99.36

Strain: lineage4.1.2.1

Drug-resistance: RR-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 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.98
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 761155 p.Ser450Leu missense_variant 0.97 rifampicin
pncA 2289154 c.87delC frameshift_variant 0.99 pyrazinamide
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 0.99
mshA 575679 p.Asn111Ser missense_variant 0.99
rpoB 760115 c.309C>T synonymous_variant 0.97
rpoC 765150 p.Gly594Glu missense_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.21
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.21
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.21
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.22
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.12
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.13
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.15
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.14
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.12
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.12
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.11
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289957 c.-716G>T upstream_gene_variant 0.99
kasA 2518076 c.-39C>T upstream_gene_variant 0.99
ahpC 2726142 c.-51G>A upstream_gene_variant 0.99
thyA 3073806 c.666C>G synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338594 c.-73T>G upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>G upstream_gene_variant 0.79
whiB6 4338602 c.-81A>T upstream_gene_variant 0.79