TB-Profiler result

Run: SRR3732645
Summary

Run ID: SRR3732645

Sample name:

Date: 04-04-2023 05:36:58

Number of reads: 1647826

Percentage reads mapped: 99.53

Strain: lineage4.3.3

Drug-resistance: MDR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289231 p.Leu4Ser missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8774 c.1473C>T synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620123 p.Arg78Leu missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765463 p.Asn698Lys missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777587 c.894G>A synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472724 n.879G>T non_coding_transcript_exon_variant 0.29
rrs 1473275 n.1430C>A non_coding_transcript_exon_variant 0.12
rrl 1473920 n.263G>T non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102401 c.642T>C synonymous_variant 0.14
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2169890 c.723C>T synonymous_variant 0.17
PPE35 2169893 c.720C>A synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2170142 c.471G>C synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289545 c.-304T>C upstream_gene_variant 0.11
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2715581 c.-249C>A upstream_gene_variant 0.15
pepQ 2859863 p.Asp186Tyr 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
fbiB 3641958 p.Val142Ile missense_variant 0.18
fbiB 3642648 p.Met372Val missense_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038392 c.2312delG frameshift_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.12
embC 4240275 p.Pro138Leu missense_variant 0.12
embC 4241693 p.Ala611Thr missense_variant 0.18
embC 4242182 p.Ala774Ser missense_variant 1.0
embC 4242366 p.Ser835Tyr missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244184 p.Ser318Arg missense_variant 0.11
embA 4244839 p.Leu536Pro missense_variant 0.15
embA 4245915 p.Gln895* stop_gained 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0