TB-Profiler result

Run: SRR4034281
Summary

Run ID: SRR4034281

Sample name:

Date: 04-04-2023 06:41:13

Number of reads: 946575

Percentage reads mapped: 99.59

Strain: lineage4.3.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
ethA 4327113 p.Gln121* stop_gained 0.12 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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9251 c.1950G>T synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575307 c.-41G>T upstream_gene_variant 0.25
ccsA 620281 c.392delG frameshift_variant 0.13
rpoB 762510 p.Ala902Ser missense_variant 0.13
rpoB 762566 p.Met920Ile missense_variant 0.14
rpoC 764158 c.790_791delCT frameshift_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765678 p.Arg770His missense_variant 0.11
rpoC 766132 c.2763C>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800891 p.Val28Gly missense_variant 0.12
rplC 801072 p.Asp88Glu missense_variant 0.12
fbiC 1303536 c.606G>C synonymous_variant 1.0
atpE 1461197 c.155dupC frameshift_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475275 n.1618C>A non_coding_transcript_exon_variant 0.11
rrl 1476557 n.2902delG non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918068 c.129C>T synonymous_variant 0.33
ndh 2102547 p.Arg166Trp missense_variant 0.1
katG 2154586 p.Asp509Ala missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290107 c.-866T>A upstream_gene_variant 1.0
folC 2746860 p.Ala247Thr missense_variant 0.33
ribD 2986866 p.Ala10Thr missense_variant 0.12
Rv2752c 3065833 p.Arg120His missense_variant 0.17
thyX 3067388 c.558C>A synonymous_variant 0.13
thyX 3067596 p.Val117Ala missense_variant 0.17
thyX 3067632 p.Ser105Tyr missense_variant 0.18
thyX 3067903 p.Thr15Ala missense_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474166 p.Ala54Thr missense_variant 0.22
fprA 3474239 p.Phe78Tyr missense_variant 0.12
whiB7 3568713 c.-34C>T upstream_gene_variant 0.12
alr 3840775 p.Thr216Ala missense_variant 0.11
alr 3840890 c.531C>A synonymous_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240189 c.327G>A synonymous_variant 0.11
embC 4240225 c.363G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248615 p.Ala701Glu missense_variant 0.1
aftB 4267880 c.957C>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0