TB-Profiler result

Run: SRR14164445
Summary

Run ID: SRR14164445

Sample name:

Date: 03-04-2023 09:52:04

Number of reads: 1510809

Percentage reads mapped: 99.58

Strain: lineage4.1.2.1

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
gid 4407759 p.Trp148* stop_gained 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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.44
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760555 p.Glu250Gly missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767008 c.3639G>A synonymous_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302920 c.-11G>A upstream_gene_variant 1.0
fbiC 1303851 c.921C>T synonymous_variant 0.1
Rv1258c 1406950 p.Ala131Thr missense_variant 0.25
atpE 1461062 c.18T>G synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471761 n.-85G>T upstream_gene_variant 0.13
rrl 1474328 n.671T>C non_coding_transcript_exon_variant 0.17
rrl 1475490 n.1833C>T non_coding_transcript_exon_variant 0.11
rrl 1476348 n.2691A>G non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169786 p.Asn276Ser missense_variant 0.12
Rv1979c 2223108 c.57C>G synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518128 p.Ser5Phe missense_variant 0.12
kasA 2518146 p.Phe11Tyr missense_variant 0.12
eis 2715470 c.-138G>A upstream_gene_variant 0.14
folC 2746277 p.Asp441Gly missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568877 c.-198C>A upstream_gene_variant 0.17
Rv3236c 3612338 p.Arg260His missense_variant 1.0
alr 3841169 c.252C>T synonymous_variant 0.12
alr 3841175 c.246G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244279 c.1047G>A synonymous_variant 0.2
embB 4248319 c.1806A>T synonymous_variant 0.31
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408275 c.-73G>A upstream_gene_variant 0.15