TB-Profiler result

Run: ERR4821147
Summary

Run ID: ERR4821147

Sample name:

Date: 01-04-2023 17:05:16

Number of reads: 841841

Percentage reads mapped: 99.64

Strain: lineage4.6.1.1

Drug-resistance: RR-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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.1 Euro-American T2-Uganda RD724 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
rpoB 761094 p.Leu430Val missense_variant 0.13 rifampicin
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 7539 p.Thr80Ala missense_variant 1.0
gyrA 7571 c.270G>A synonymous_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8358 p.Pro353Ser missense_variant 0.13
gyrA 9013 p.Thr571Asn missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.2
rpoB 759620 c.-187A>C upstream_gene_variant 0.17
rpoB 761055 p.Val417Met missense_variant 0.11
rpoB 762386 p.Asn860Lys missense_variant 0.12
rpoC 764114 p.Gly249Ser missense_variant 0.13
rpoC 767133 p.Gly1255Val missense_variant 0.13
rpoC 767150 p.Gly1261Ser missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776097 p.Thr795Asn missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304503 c.1573C>T synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674222 c.24delA frameshift_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153905 p.Arg736Lys missense_variant 0.2
katG 2154688 p.Thr475Ile missense_variant 0.17
katG 2155528 p.Glu195Gly missense_variant 0.18
PPE35 2170147 p.Ser156Ala missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289937 c.-696C>T upstream_gene_variant 0.13
kasA 2518348 c.234A>T synonymous_variant 0.12
eis 2714935 p.Pro133His missense_variant 0.14
ahpC 2726338 p.Val49Gly missense_variant 0.34
pepQ 2859386 p.Ala345Ser missense_variant 0.11
Rv2752c 3065576 p.Ala206Thr missense_variant 0.11
ald 3087327 p.Asp170Asn missense_variant 0.12
ald 3087504 p.Val229Ile missense_variant 0.11
Rv3083 3448821 c.318C>T synonymous_variant 0.2
Rv3083 3449234 p.Arg244His missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474898 p.Gly298Ser missense_variant 0.17
fbiA 3641270 p.Tyr243Phe missense_variant 0.1
fbiB 3642801 p.Ala423Pro missense_variant 0.17
alr 3840523 p.Ile300Val missense_variant 0.1
rpoA 3878527 c.-20C>G upstream_gene_variant 0.5
clpC1 4038729 p.Asn659Ser missense_variant 0.1
clpC1 4038734 p.Phe657Leu missense_variant 0.12
clpC1 4038738 p.Asp656Val missense_variant 0.22
clpC1 4039508 c.1197G>C synonymous_variant 0.25
clpC1 4040414 c.291G>A synonymous_variant 0.1
panD 4044130 p.Asn51Ile missense_variant 0.12
embC 4242420 p.Ser853Thr missense_variant 0.14
embC 4242421 c.2562_2580delGCGAGCCGGCGTGCAGGTG frameshift_variant 0.15
embC 4242444 p.Pro861His missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246249 p.Arg1006Gln missense_variant 0.15
embB 4246777 c.264G>T synonymous_variant 0.13
embB 4246953 p.Arg147His missense_variant 0.13
embB 4247768 p.Ile419Val missense_variant 0.1
embB 4249234 c.2721C>A synonymous_variant 0.11
aftB 4268624 c.213C>T synonymous_variant 0.5
ubiA 4268986 c.847delG frameshift_variant 0.29
ubiA 4269202 p.Glu211Gly missense_variant 0.12
ethR 4327780 p.Arg78Trp missense_variant 0.13
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0