TB-Profiler result

Run: ERR2229093
Summary

Run ID: ERR2229093

Sample name:

Date: 31-03-2023 16:38:03

Number of reads: 310345

Percentage reads mapped: 99.35

Strain: lineage4.8

Drug-resistance: HR-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
lineage4.8 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
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 0.29 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155060 p.Trp351* stop_gained 0.18 isoniazid
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 7070 p.Lys611* stop_gained 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7609 p.Trp103* stop_gained 0.18
gyrA 8331 p.Asn344Tyr missense_variant 0.14
gyrA 8957 c.1656C>T synonymous_variant 0.15
mshA 575386 c.39C>T synonymous_variant 0.33
rpoC 764848 p.Glu493Asp missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801302 p.Arg165Gln missense_variant 0.4
fbiC 1303678 p.Arg250Trp missense_variant 0.33
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416208 c.1140C>A synonymous_variant 0.12
embR 1416660 p.Arg230Gly missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471771 n.-74delG upstream_gene_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474976 n.1319G>T non_coding_transcript_exon_variant 0.5
fabG1 1673380 c.-60C>G upstream_gene_variant 0.5
inhA 1674967 p.Asp256His missense_variant 0.12
rpsA 1834063 c.522C>T synonymous_variant 0.18
rpsA 1834706 p.Asn389Asp missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156237 c.-126A>G upstream_gene_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.17
PPE35 2167967 c.2646A>C synonymous_variant 0.17
PPE35 2168151 p.Thr821Asn missense_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169403 p.Thr404Pro missense_variant 0.22
PPE35 2169581 c.1032C>G synonymous_variant 0.22
PPE35 2169587 c.1026G>A synonymous_variant 0.25
PPE35 2169602 c.1011C>A synonymous_variant 0.25
PPE35 2169623 c.990T>C synonymous_variant 0.25
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.12
PPE35 2170159 p.Ala152Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519098 c.984C>A synonymous_variant 0.25
eis 2715155 p.Gly60Trp missense_variant 0.67
Rv2752c 3065789 c.403C>A synonymous_variant 0.22
fbiA 3640477 c.-66C>A upstream_gene_variant 0.2
clpC1 4038974 c.1731T>C synonymous_variant 1.0
clpC1 4039036 p.Val557Phe missense_variant 0.5
panD 4043974 p.Pro103Leu missense_variant 0.33
panD 4044412 c.-131C>T upstream_gene_variant 1.0
embC 4241002 c.1140G>T synonymous_variant 0.2
embC 4241889 p.Ala676Glu missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242992 p.Thr1044Ala missense_variant 0.25
embA 4243253 p.Glu7Asp missense_variant 0.29
embB 4246990 c.477C>A synonymous_variant 0.5
embB 4247719 c.1206G>A synonymous_variant 0.33
embB 4247748 p.Ser412* stop_gained 0.5
embB 4248685 c.2172C>T synonymous_variant 0.25
embB 4249744 c.3231G>A synonymous_variant 0.4
embB 4249751 c.3238T>C synonymous_variant 0.4
ethR 4326610 c.-939G>T upstream_gene_variant 0.67
ethA 4326980 p.Gln165Arg missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407894 c.309G>A synonymous_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0