TB-Profiler result

Run: ERR11043121
Summary

Run ID: ERR11043121

Sample name:

Date: 31-03-2023 11:28:18

Number of reads: 1961741

Percentage reads mapped: 99.58

Strain: lineage4.6.5

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.5 Euro-American T;LAM 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.Ser450Leu missense_variant 1.0 rifampicin
tlyA 1918647 p.Asn236Lys missense_variant 1.0 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289038 p.Trp68Cys missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile 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
gyrB 5489 p.Ile84Val missense_variant 1.0
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 490756 c.-27T>G upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777974 c.507C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.31
rrs 1471900 n.55C>T non_coding_transcript_exon_variant 0.31
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.16
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.23
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.23
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.21
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.22
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.15
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.17
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.16
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.16
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.21
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.17
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.18
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.18
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.19
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.15
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.18
fabG1 1673349 c.-91G>C upstream_gene_variant 0.18
fabG1 1673357 c.-83G>A upstream_gene_variant 0.22
fabG1 1673359 c.-81T>C upstream_gene_variant 0.22
fabG1 1673361 c.-79C>G upstream_gene_variant 0.23
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167814 c.2799C>T synonymous_variant 0.23
PPE35 2167825 c.2780_2787delTGCTAGCC frameshift_variant 0.2
PPE35 2169902 p.Leu237Phe missense_variant 0.28
PPE35 2169910 p.Asn235Tyr missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.15
folC 2746995 p.Val202Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640346 c.-196delA upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.18
clpC1 4038332 c.2373C>T synonymous_variant 1.0
clpC1 4039018 p.Ser563Ala missense_variant 0.29
clpC1 4039022 c.1683A>G synonymous_variant 0.29
clpC1 4039031 c.1674T>C synonymous_variant 0.27
clpC1 4039829 p.Leu292Phe missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4247090 p.Thr193Ala missense_variant 0.21
embB 4247098 c.585C>G synonymous_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0