TB-Profiler result

Run: SRR924238
Summary

Run ID: SRR924238

Sample name:

Date: 04-04-2023 22:25:44

Number of reads: 1083850

Percentage reads mapped: 93.77

Strain: lineage4

Drug-resistance: MDR-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
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.Ser450Trp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288823 p.Arg140Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491556 p.Gln258His missense_variant 0.18
fgd1 491557 c.780_784dupCAGCA frameshift_variant 0.18
fgd1 491569 p.Asp263Asn missense_variant 0.17
mshA 575701 p.Glu118Asp missense_variant 0.4
rpoB 760028 c.222C>A synonymous_variant 0.17
rpoB 760496 c.690G>T synonymous_variant 0.19
rpoB 761032 p.Gln409Arg missense_variant 1.0
rpoB 762506 p.Phe900Leu missense_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781619 p.Lys20Asn missense_variant 0.12
fbiC 1305205 p.Pro759Thr missense_variant 0.15
Rv1258c 1406351 c.990G>T synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471669 n.-177_-176insG upstream_gene_variant 0.18
rrs 1472447 n.602C>A non_coding_transcript_exon_variant 0.2
rrl 1474282 n.625G>T non_coding_transcript_exon_variant 0.23
rrl 1475321 n.1664G>T non_coding_transcript_exon_variant 0.22
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
fabG1 1673783 p.Gly115Val missense_variant 0.17
inhA 1673988 c.-214G>T upstream_gene_variant 0.17
ndh 2102422 c.621C>A synonymous_variant 0.4
Rv1979c 2222247 c.918C>A synonymous_variant 0.18
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290005 c.-764G>T upstream_gene_variant 0.33
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714795 p.Glu180* stop_gained 0.15
eis 2715244 p.Pro30His missense_variant 0.33
ahpC 2726323 p.Pro44Gln missense_variant 0.2
pepQ 2859604 p.Gly272Val missense_variant 0.5
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449147 p.Ser215* stop_gained 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474044 p.Pro13Leu missense_variant 0.18
rpoA 3878641 c.-135delG upstream_gene_variant 0.5
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038842 c.1863G>T synonymous_variant 0.22
clpC1 4038871 p.Glu612* stop_gained 0.17
clpC1 4040088 c.615_616dupTC frameshift_variant 0.14
embC 4239863 c.1A>G start_lost 1.0
embB 4249762 c.3249G>T synonymous_variant 0.17
ethR 4327745 p.Pro66Gln missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0