TB-Profiler result

Run: SRR4033470
Summary

Run ID: SRR4033470

Sample name:

Date: 04-04-2023 06:07:10

Number of reads: 1400683

Percentage reads mapped: 99.66

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 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
mmpR5 779191 p.Ser68Gly missense_variant 0.11 clofazimine, bedaquiline
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 5087 c.-153C>T upstream_gene_variant 0.22
gyrB 5096 c.-144A>G upstream_gene_variant 0.22
gyrB 5420 p.Tyr61His missense_variant 0.12
gyrB 5485 c.246C>G synonymous_variant 0.15
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 9085 p.His595Arg missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490941 c.160delT frameshift_variant 0.11
rpoB 763000 p.Met1065Thr missense_variant 0.12
rpoC 764223 p.Lys285Arg missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777272 c.1209C>A synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781539 c.-21C>T upstream_gene_variant 0.12
rplC 801436 p.Ser210Gly missense_variant 0.11
fbiC 1304192 p.Ala421Val missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471818 n.-28G>A upstream_gene_variant 0.18
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1476197 n.2540T>A non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103184 c.-142G>C upstream_gene_variant 0.12
PPE35 2167855 p.Phe920Leu missense_variant 0.12
PPE35 2169574 p.Phe347Ile missense_variant 0.12
PPE35 2169625 p.Gly330Arg missense_variant 0.11
PPE35 2169628 p.Ile329Val missense_variant 0.13
PPE35 2169759 p.Gly285Ala missense_variant 0.12
Rv1979c 2223248 c.-84G>A upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726696 c.504C>T synonymous_variant 0.13
ahpC 2726712 p.Cys174Arg missense_variant 0.13
thyX 3067830 p.Ala39Val missense_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339747 c.630G>A synonymous_variant 0.2
fprA 3473879 c.-128T>C upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242581 p.Ala907Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246049 c.-465G>A upstream_gene_variant 0.13
ethR 4327688 p.Val47Ala missense_variant 0.11
ethA 4327696 c.-223G>A upstream_gene_variant 0.12
ethR 4327700 p.Ala51Gly missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0