TB-Profiler result

Run: ERR4812968
Summary

Run ID: ERR4812968

Sample name:

Date: 01-04-2023 12:27:00

Number of reads: 462081

Percentage reads mapped: 51.13

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
pncA 2289090 p.His51Arg missense_variant 0.2 pyrazinamide
pncA 2289213 p.Gln10Arg missense_variant 0.85 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.92 ethambutol
gid 4407952 p.Pro84Leu missense_variant 0.96 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
gyrB 5507 p.Ala90Thr missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762211 p.Pro802Arg missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766487 p.Pro1040Ala missense_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.12
mmpL5 776182 p.Asp767Asn missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801258 c.450C>A synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.25
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.25
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.25
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.25
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.22
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.22
rrs 1472130 n.285G>C non_coding_transcript_exon_variant 0.22
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.2
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.18
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.2
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.27
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.25
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.23
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.23
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.15
fabG1 1674094 p.Gly219Arg missense_variant 0.2
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.83
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168998 p.Ile539Val missense_variant 1.0
PPE35 2169006 p.Ser536Leu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726728 p.Arg179His missense_variant 0.22
folC 2746149 p.Arg484Cys missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338978 c.-140C>T upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474047 p.Ser14Leu missense_variant 0.11
fbiB 3641789 c.255G>T synonymous_variant 0.22
alr 3841433 c.-13G>A upstream_gene_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038434 c.2271G>T synonymous_variant 0.13
panD 4044140 p.Asp48Tyr missense_variant 0.18
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246235 c.-279G>A upstream_gene_variant 0.14
embA 4246253 p.Ile1007Met missense_variant 0.22
embB 4248613 c.2100C>A synonymous_variant 0.12
ubiA 4269058 p.Ile259Thr missense_variant 0.13
ubiA 4269565 p.Arg90Gln missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0