TB-Profiler result

Run: SRR1002685

Summary

Run ID: SRR1002685

Sample name:

Date: 02-04-2023 14:19:38

Number of reads: 924783

Percentage reads mapped: 98.21

Strain: lineage4.3.3

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 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155790 c.321delG frameshift_variant 0.12 isoniazid
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 9304 p.Gly668Asp missense_variant 1.0
mshA 575619 p.Arg91Leu missense_variant 0.14
mshA 576296 p.Asp317Asn missense_variant 0.2
rpoB 761060 c.1254C>A synonymous_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302742 c.-189G>T upstream_gene_variant 0.14
fbiC 1303095 c.165G>A synonymous_variant 1.0
fbiC 1304962 p.Trp678Gly missense_variant 1.0
Rv1258c 1406908 p.Ala145Ser missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918181 p.Val81Ala missense_variant 0.12
tlyA 1918429 c.490T>C synonymous_variant 1.0
ndh 2102687 p.Ala119Glu missense_variant 0.12
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.18
PPE35 2167868 c.2745A>C synonymous_variant 0.16
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2169269 c.1344A>G synonymous_variant 0.15
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2169278 c.1335T>C synonymous_variant 0.2
PPE35 2169281 c.1332T>G synonymous_variant 0.19
PPE35 2169725 c.888T>C synonymous_variant 0.12
PPE35 2170235 c.378T>C synonymous_variant 0.11
PPE35 2170238 c.375T>G synonymous_variant 0.11
PPE35 2170244 c.369G>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519143 c.1029G>C synonymous_variant 0.1
kasA 2519208 p.Gly365Asp missense_variant 0.12
folC 2746340 p.Ala420Val missense_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339268 c.152_153insTTCGTC disruptive_inframe_insertion 0.18
fbiD 3339273 c.156T>G synonymous_variant 0.33
fbiD 3339275 c.159_160delCG frameshift_variant 0.25
fbiD 3339279 c.162T>A synonymous_variant 0.25
fbiD 3339281 p.Ser55* stop_gained 0.25
fbiD 3339284 p.Leu56Gln missense_variant 0.25
fbiD 3339286 p.Arg57* stop_gained 0.27
fbiD 3339293 p.Ile59Ser missense_variant 0.27
fbiD 3339295 p.Thr60Ala missense_variant 0.3
fbiD 3339300 c.183T>G synonymous_variant 0.27
fbiD 3339302 p.Ile62Asn missense_variant 0.27
fbiD 3339303 c.186_187insCG frameshift_variant 0.27
fbiD 3339306 c.189C>A synonymous_variant 0.3
fbiD 3339309 c.194_199delACGAAG disruptive_inframe_deletion 0.27
fbiD 3339682 p.Val189Leu missense_variant 0.11
Rv3083 3449758 p.Thr419Ala missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878565 c.-58G>T upstream_gene_variant 0.33
rpoA 3878627 c.-120T>G upstream_gene_variant 0.4
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243358 c.126C>T synonymous_variant 0.14
embB 4247470 c.957T>C synonymous_variant 0.24
embB 4247472 p.Phe320Tyr missense_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0