TB-Profiler result

Run: SRR6982315
Summary

Run ID: SRR6982315

Sample name:

Date: 04-04-2023 18:33:46

Number of reads: 266532

Percentage reads mapped: 99.67

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
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.99
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
gid 4407880 p.Leu108Arg missense_variant 0.2 streptomycin
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 8445 p.Arg382Cys missense_variant 0.1
gyrA 8765 c.1464C>T synonymous_variant 0.13
gyrA 8793 p.Ile498Val missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9793 p.Asn831Ile missense_variant 0.18
rpoB 759633 c.-174C>T upstream_gene_variant 0.25
rpoB 759702 c.-105_-104insCG upstream_gene_variant 0.2
rpoB 759767 c.-40G>T upstream_gene_variant 0.22
rpoC 763412 p.Ala15Ser missense_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778611 p.Ala99Ser missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303631 p.Pro234His missense_variant 0.2
Rv1258c 1406271 c.1069delT frameshift_variant 0.13
Rv1258c 1406449 p.Leu298Met missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472249 n.409delG non_coding_transcript_exon_variant 0.13
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475693 n.2036A>G non_coding_transcript_exon_variant 0.1
rrl 1476548 n.2891T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918120 p.Ala61Thr missense_variant 0.12
tlyA 1918516 p.Gly193Cys missense_variant 0.67
katG 2155672 p.Leu147Gln missense_variant 0.22
katG 2156382 c.-271A>G upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715309 c.24G>A synonymous_variant 0.15
ahpC 2726172 c.-21G>A upstream_gene_variant 0.22
Rv2752c 3065774 p.Glu140* stop_gained 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073916 p.His186Asn missense_variant 0.25
thyA 3074295 c.177G>A synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.29
Rv3083 3448865 p.Val121Ala missense_variant 0.2
fprA 3473959 c.-48A>G upstream_gene_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641434 p.Ile298Val missense_variant 0.17
fbiB 3642676 p.Val381Ala missense_variant 0.15
rpoA 3878074 p.Gly145Val missense_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044227 p.Asp19Asn missense_variant 0.18
embC 4241975 p.Gln705Glu missense_variant 0.18
embC 4242026 p.Ser722Pro missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243096 c.-137A>G upstream_gene_variant 0.33
embA 4243148 c.-85A>G upstream_gene_variant 0.25
embA 4244300 c.1070delA frameshift_variant 0.22
embB 4247482 c.969C>T synonymous_variant 0.1
embB 4247948 c.1436dupT frameshift_variant 0.12
aftB 4268404 c.433T>C synonymous_variant 0.13
ethA 4326048 p.Glu476Lys missense_variant 0.13
whiB6 4338421 p.Cys34Tyr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0