TB-Profiler result

Run: ERR5866287
Summary

Run ID: ERR5866287

Sample name:

Date: 02-04-2023 00:36:25

Number of reads: 620649

Percentage reads mapped: 98.74

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
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
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288817 p.Thr142Met missense_variant 0.75 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8072 c.772delG frameshift_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619914 c.24C>T synonymous_variant 0.17
rpoC 764196 p.Ser276* stop_gained 0.22
rpoC 764918 p.Val517Leu missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775994 c.2487C>T synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 1.0
atpE 1461203 c.159C>T synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.14
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.15
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.2
rpsA 1833813 p.Leu91His missense_variant 0.12
rpsA 1834836 p.Met432Thr missense_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
katG 2156475 c.-364A>T upstream_gene_variant 0.1
PPE35 2169488 c.1125G>C synonymous_variant 0.2
PPE35 2169491 c.1122T>C synonymous_variant 0.2
Rv1979c 2223044 p.Gly41Arg missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val missense_variant 1.0
Rv2752c 3066290 c.-99G>A upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449534 p.Thr344Ile missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 0.11
alr 3840712 p.Ser237Pro missense_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embC 4240682 p.Asp274Asn missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244001 p.Val257Met missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407857 p.Arg116Trp missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0