TB-Profiler result

Run: SRR4037854
Summary

Run ID: SRR4037854

Sample name:

Date: 04-04-2023 07:43:13

Number of reads: 465508

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
lineage4.3.2.1 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 4326609 c.864delC frameshift_variant 0.17 ethionamide, 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 7799 c.498A>C synonymous_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9760 p.Glu820Val missense_variant 0.4
rpoB 762486 p.Pro894Ser missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766881 p.Gly1171Asp missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777634 p.Gly283Ser missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472174 n.329C>T non_coding_transcript_exon_variant 0.14
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472857 n.1012A>T non_coding_transcript_exon_variant 0.12
rrl 1474795 n.1138A>T non_coding_transcript_exon_variant 0.13
rpsA 1834462 c.921C>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.17
Rv1979c 2221735 p.Arg477Gln missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518955 p.Ala281Thr missense_variant 0.33
thyX 3067931 c.15G>A synonymous_variant 0.29
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
fbiB 3641681 c.147C>T synonymous_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241436 p.Ala525Asp missense_variant 0.4
embC 4241689 c.1827G>T synonymous_variant 0.15
embC 4242320 p.Pro820Ser missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242901 c.-332G>T upstream_gene_variant 0.13
embB 4248009 p.Leu499Pro missense_variant 0.18
aftB 4268030 c.807G>A synonymous_variant 0.22
ubiA 4269870 c.-37C>T upstream_gene_variant 0.33
ethA 4326629 p.Phe282Ser missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0