TB-Profiler result

Run: ERR228213

Summary

Run ID: ERR228213

Sample name:

Date: 31-03-2023 17:48:52

Number of reads: 3137823

Percentage reads mapped: 99.34

Strain: lineage4;lineage3

Drug-resistance: Other


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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 0.85
lineage4 Euro-American LAM;T;S;X;H None 0.18
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 0.14 streptomycin
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 0.87
gyrA 9304 p.Gly668Asp missense_variant 0.88
fgd1 491742 c.960T>C synonymous_variant 0.86
rpoC 762434 c.-936T>G upstream_gene_variant 0.89
rpoC 763031 c.-339T>C upstream_gene_variant 0.87
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.81
mmpL5 778107 p.Ser125Cys missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.23
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153933 p.Ala727Ser missense_variant 0.21
katG 2154724 p.Arg463Leu missense_variant 0.92
PPE35 2167926 p.Leu896Ser missense_variant 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.91
ahpC 2726105 c.-88G>A upstream_gene_variant 0.84
ald 3086788 c.-32T>C upstream_gene_variant 0.9
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.96
fbiB 3642098 c.564G>A synonymous_variant 0.7
alr 3840636 p.Pro262Gln missense_variant 0.86
rpoA 3878622 c.-115C>G upstream_gene_variant 0.74
embC 4241335 p.Gln491His missense_variant 0.72
embC 4242075 p.Arg738Gln missense_variant 0.91
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245883 p.Gly884Asp missense_variant 0.75
embB 4248561 p.Ala683Val missense_variant 0.83
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.87