TB-Profiler result

Run: ERR4817347
Summary

Run ID: ERR4817347

Sample name:

Date: 01-04-2023 14:56:33

Number of reads: 112879

Percentage reads mapped: 66.2

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 0.93
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
fabG1 1673423 c.-17G>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 5389 c.150C>T synonymous_variant 0.5
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 1.0
gyrA 9242 c.1941A>C synonymous_variant 0.4
gyrA 9252 p.Val651Ile missense_variant 0.67
gyrA 9275 c.1974G>A synonymous_variant 1.0
gyrA 9278 c.1977G>C synonymous_variant 1.0
gyrA 9281 c.1980C>G synonymous_variant 1.0
gyrA 9284 c.1983T>C synonymous_variant 1.0
gyrA 9291 c.1990C>T synonymous_variant 1.0
fgd1 491125 p.Ala115Thr missense_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781531 c.-29T>G upstream_gene_variant 0.5
rplC 800725 c.-84C>T upstream_gene_variant 0.5
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102433 p.Ile204Phe missense_variant 0.5
ndh 2102497 c.546T>G synonymous_variant 0.67
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169369 p.Gly415Ala missense_variant 1.0
PPE35 2170432 p.Ser61Ala missense_variant 0.67
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290199 c.-958C>G upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859506 p.Ala305Ser missense_variant 0.4
thyA 3073863 c.609T>C synonymous_variant 0.5
thyA 3073872 p.Ile200Val missense_variant 0.4
thyA 3073878 c.594G>A synonymous_variant 0.4
thyA 3073892 c.580T>C synonymous_variant 0.33
thyA 3073893 c.579C>G synonymous_variant 0.33
thyA 3073902 c.570C>G synonymous_variant 0.33
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
panD 4044247 p.Arg12Pro missense_variant 0.33
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244840 c.1608G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0