TB-Profiler result

Run: ERR987753
Summary

Run ID: ERR987753

Sample name:

Date: 02-04-2023 13:23:50

Number of reads: 13176850

Percentage reads mapped: 99.44

Strain: lineage4.6.1.2;lineage4.2;lineage3

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
lineage3 East-African-Indian CAS RD750 0.81
lineage4 Euro-American LAM;T;S;X;H None 0.18
lineage4.6 Euro-American T;LAM None 0.11
lineage4.2 Euro-American H;T;LAM None 0.05
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.11
lineage4.6.1.2 Euro-American T2 RD724 0.11
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
rpsL 781687 p.Lys43Arg missense_variant 0.11 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.25 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.78
rpoC 762434 c.-936T>G upstream_gene_variant 0.77
rpoC 763031 c.-339T>C upstream_gene_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.82
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.87
rrl 1476758 n.3101G>C non_coding_transcript_exon_variant 0.79
fabG1 1673152 c.-288A>G upstream_gene_variant 0.14
inhA 1674465 c.264C>T synonymous_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.81
PPE35 2167926 p.Leu896Ser missense_variant 0.85
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.82
kasA 2518586 p.Leu158Phe missense_variant 0.1
ahpC 2726105 c.-88G>A upstream_gene_variant 0.85
thyA 3073806 c.666C>G synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 0.91
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642098 c.564G>A synonymous_variant 0.77
alr 3840636 p.Pro262Gln missense_variant 0.8
rpoA 3878622 c.-115C>G upstream_gene_variant 0.88
embC 4242075 p.Arg738Gln missense_variant 0.74
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 0.11
embA 4245883 p.Gly884Asp missense_variant 0.8
ethA 4326230 p.Asp415Gly missense_variant 0.83
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 0.1
gid 4407588 c.615A>G synonymous_variant 0.81