TB-Profiler result

Run: SRR22424890
Summary

Run ID: SRR22424890

Sample name:

Date: 04-04-2023 04:15:48

Number of reads: 1168034

Percentage reads mapped: 99.63

Strain: lineage4.8

Drug-resistance: MDR-TB

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288718 p.Met175Arg missense_variant 1.0 pyrazinamide
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
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 6625 c.-677G>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8104 p.Ser268* stop_gained 0.14
rpoB 761461 p.Arg552His missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305009 c.2079C>A synonymous_variant 0.12
Rv1258c 1407446 c.-106G>A upstream_gene_variant 0.11
atpE 1461059 c.15C>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472018 n.173G>T non_coding_transcript_exon_variant 0.15
rrs 1472096 n.251T>A non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474185 n.528G>T non_coding_transcript_exon_variant 0.33
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168182 p.Leu811Ile missense_variant 0.12
PPE35 2168265 p.Gly783Glu missense_variant 1.0
PPE35 2169752 c.860delT frameshift_variant 0.12
PPE35 2170317 p.Ala99Val missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289682 c.-441C>A upstream_gene_variant 0.11
fprA 3474604 p.Arg200* stop_gained 0.12
fbiB 3641709 p.Arg59Trp missense_variant 0.12
rpoA 3878133 c.375C>A synonymous_variant 0.14
rpoA 3878656 c.-149C>A upstream_gene_variant 0.5
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0