TB-Profiler result

Run: ERR2229597

Summary

Run ID: ERR2229597

Sample name:

Date: 31-03-2023 17:20:39

Number of reads: 325204

Percentage reads mapped: 99.17

Strain: lineage4

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
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
katG 2155740 c.371delG frameshift_variant 0.13 isoniazid, 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7593 p.Arg98Cys missense_variant 0.15
mshA 575590 c.243T>G synonymous_variant 0.33
mshA 576418 c.1071G>A synonymous_variant 0.18
rpoB 760129 p.Asp108Gly missense_variant 0.2
rpoB 762340 p.Arg845Leu missense_variant 0.29
rpoB 763302 c.3497delC frameshift_variant 0.4
rpoC 763919 p.Leu184Val missense_variant 0.25
rpoC 764318 p.Val317Phe missense_variant 1.0
rpoC 765449 p.Ala694Thr missense_variant 0.67
rpoC 765692 p.Val775Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302832 c.-99G>A upstream_gene_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303795 p.Glu289Lys missense_variant 0.2
fbiC 1305007 p.Ile693Phe missense_variant 0.29
embR 1416708 p.Ala214Thr missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472998 n.1153C>T non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474564 n.907G>A non_coding_transcript_exon_variant 0.14
rpsA 1834342 p.Met267Ile missense_variant 0.12
rpsA 1834362 p.Leu274* stop_gained 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154420 c.1692G>A synonymous_variant 0.4
katG 2154838 p.Arg425Ile missense_variant 0.33
katG 2156450 c.-339T>A upstream_gene_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168987 c.1626A>C synonymous_variant 0.33
PPE35 2169440 c.1173C>T synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.77
PPE35 2170053 p.Thr187Ser missense_variant 0.79
PPE35 2170147 p.Ser156Ala missense_variant 0.14
PPE35 2170157 p.Ala152Ser missense_variant 0.26
PPE35 2170220 c.393C>G synonymous_variant 0.12
PPE35 2170223 c.390T>C synonymous_variant 0.12
PPE35 2170232 c.381T>C synonymous_variant 0.12
PPE35 2170235 p.Phe126Leu missense_variant 0.12
PPE35 2170238 c.375T>G synonymous_variant 0.12
PPE35 2170527 p.Ser29Val missense_variant 0.14
Rv1979c 2223274 c.-110A>G upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289314 c.-73T>C upstream_gene_variant 0.12
kasA 2517969 c.-146C>T upstream_gene_variant 0.4
eis 2714533 p.Ile267Asn missense_variant 0.25
ahpC 2725930 c.-263C>T upstream_gene_variant 0.22
folC 2746683 p.Leu306Ile missense_variant 0.33
folC 2746929 p.Pro224Thr missense_variant 0.33
thyA 3073954 p.Gly173Asp missense_variant 0.12
ald 3087790 p.Leu324His missense_variant 0.29
fprA 3474558 c.552A>G synonymous_variant 0.33
fbiA 3641243 p.Arg234Gln missense_variant 0.33
fbiB 3642104 c.570C>T synonymous_variant 0.4
alr 3841546 c.-126C>A upstream_gene_variant 0.45
rpoA 3878068 p.Val147Ala missense_variant 0.14
rpoA 3878124 c.384G>T synonymous_variant 0.18
clpC1 4040094 p.Leu204Arg missense_variant 0.33
embC 4239697 c.-166A>T upstream_gene_variant 0.22
embA 4242349 c.-884A>C upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243587 p.Arg119Cys missense_variant 0.2
embA 4244415 c.1187_1189delTGG disruptive_inframe_deletion 0.17
embB 4247814 p.Ala434Asp missense_variant 0.17
embB 4248049 c.1536C>T synonymous_variant 0.25
embB 4249486 c.2973T>G synonymous_variant 0.29
ethA 4326557 p.Arg306Leu missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0