TB-Profiler result

Run: ERR1213918
Summary

Run ID: ERR1213918

Sample name:

Date: 31-03-2023 12:44:15

Number of reads: 1862677

Percentage reads mapped: 99.02

Strain: lineage4.6.2

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 0.99
lineage4.6 Euro-American T;LAM None 0.83
lineage4.6.2 Euro-American T;LAM RD726 0.85
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 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
gyrB 5325 p.Arg29Leu missense_variant 0.2
gyrB 7196 p.Gly653Cys missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 0.17
gyrA 8397 p.Val366Ile missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759939 p.Pro45Ala missense_variant 0.71
rpoC 762836 c.-534C>G upstream_gene_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776683 c.1798C>T synonymous_variant 0.22
mmpL5 777647 c.834C>A synonymous_variant 0.33
mmpR5 778298 c.-692C>T upstream_gene_variant 0.94
fbiC 1304723 p.Glu598Val missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 0.82
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.17
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.18
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.17
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.15
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.15
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.18
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.43
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.43
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.21
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.2
rrl 1476746 n.3089T>A non_coding_transcript_exon_variant 0.12
rrl 1476755 n.3098G>T non_coding_transcript_exon_variant 0.12
rpsA 1834118 p.Gln193* stop_gained 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 1.0
PPE35 2168499 p.Ser705Leu missense_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.54
PPE35 2169785 p.Asn276Lys missense_variant 0.12
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.6
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714130 p.Glu401Asp missense_variant 0.25
eis 2714320 p.Ala338Val missense_variant 0.25
eis 2714727 c.606A>C synonymous_variant 0.71
thyX 3067474 p.Pro158Ala missense_variant 0.67
ald 3086788 c.-32T>C upstream_gene_variant 0.15
Rv3083 3448394 c.-110G>T upstream_gene_variant 0.29
Rv3083 3448567 p.His22Asp missense_variant 0.64
Rv3083 3449882 p.Trp460* stop_gained 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612768 p.Ala117Ser missense_variant 0.25
alr 3840904 p.Pro173Ser missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247613 p.Arg367His missense_variant 0.25
embB 4247973 p.Thr487Ile missense_variant 0.22
embB 4248298 c.1785C>T synonymous_variant 0.5
embB 4248964 c.2451G>A synonymous_variant 0.33
aftB 4267272 p.Lys522Arg missense_variant 0.93
ethR 4326739 c.-810G>C upstream_gene_variant 0.75
ethA 4328004 c.-531C>T upstream_gene_variant 0.62
ethA 4328202 c.-729G>A upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 0.4