TB-Profiler result

Run: ERR2229345
Summary

Run ID: ERR2229345

Sample name:

Date: 31-03-2023 17:05:41

Number of reads: 1349853

Percentage reads mapped: 98.91

Strain: lineage4.8

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 7266 c.-36A>G upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7598 p.Met99Ile missense_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.29
mshA 576111 p.Ala255Gly missense_variant 0.13
mshA 576661 c.1314G>A synonymous_variant 0.17
rpoB 759802 c.-5G>T upstream_gene_variant 0.17
rpoB 762275 c.2469C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775704 p.Thr926Lys missense_variant 0.17
mmpL5 775927 c.2554C>T synonymous_variant 0.12
mmpL5 776027 c.2454G>A synonymous_variant 0.29
mmpL5 776030 c.2451G>A synonymous_variant 0.29
mmpL5 776036 c.2445G>T synonymous_variant 0.29
mmpL5 776848 p.Gln545Lys missense_variant 0.18
mmpL5 779076 c.-596G>A upstream_gene_variant 0.13
mmpL5 779175 c.-695G>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304077 p.Glu383Lys missense_variant 0.12
embR 1416802 c.546C>T synonymous_variant 0.12
atpE 1461145 p.Ala34Gly missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>T non_coding_transcript_exon_variant 0.14
rrs 1472565 n.720A>G non_coding_transcript_exon_variant 0.2
rrs 1473179 n.1334C>G non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474413 n.756A>T non_coding_transcript_exon_variant 0.18
rrl 1475317 n.1660G>T non_coding_transcript_exon_variant 0.14
rrl 1475475 n.1818C>A non_coding_transcript_exon_variant 0.2
fabG1 1673357 c.-83G>A upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.38
inhA 1673658 c.-544G>C upstream_gene_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155737 c.375C>A synonymous_variant 0.17
PPE35 2167878 p.Ser912Asn missense_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.2
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.65
PPE35 2170053 p.Thr187Ser missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288972 c.270C>T synonymous_variant 0.12
kasA 2518606 c.492G>C synonymous_variant 0.15
kasA 2518609 p.Met165Ile missense_variant 0.17
kasA 2518809 p.Lys232Arg missense_variant 0.11
kasA 2518864 c.750G>C synonymous_variant 0.12
folC 2746858 c.741C>A synonymous_variant 0.13
pepQ 2860184 c.229_234delCGCGCG conservative_inframe_deletion 0.17
pepQ 2860200 c.219G>A synonymous_variant 0.17
pepQ 2860201 c.216_217delAG frameshift_variant 0.2
pepQ 2860207 c.211_212insGCGCGC conservative_inframe_insertion 0.22
pepQ 2860564 c.-146A>G upstream_gene_variant 0.17
thyX 3067340 c.606G>A synonymous_variant 0.17
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3475185 c.1179C>A synonymous_variant 0.12
fprA 3475326 c.1320C>G synonymous_variant 0.22
Rv3236c 3612455 p.Arg221Leu missense_variant 0.15
Rv3236c 3612642 p.Asp159Tyr missense_variant 0.12
fbiB 3642226 p.Gln231Pro missense_variant 0.12
fbiB 3642229 p.Leu232Gln missense_variant 0.12
fbiB 3642232 p.Leu233Gln missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.24
ddn 3987034 p.Leu64His missense_variant 0.14
ddn 3987093 p.Lys84* stop_gained 0.12
clpC1 4038752 p.Gln651His missense_variant 0.17
clpC1 4039730 c.975C>G synonymous_variant 0.12
embC 4241156 p.Gly432Cys missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243414 p.Pro61Leu missense_variant 0.13
embA 4245122 c.1894delG frameshift_variant 0.22
embA 4246168 p.Met979Lys missense_variant 0.18
embA 4246288 p.Asn1019Ser missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.45
embB 4246556 p.Ala15Pro missense_variant 0.45
embB 4247160 p.Thr216Met missense_variant 0.15
embB 4249404 p.Thr964Asn missense_variant 0.14
aftB 4269252 c.-416C>A upstream_gene_variant 0.15
ethA 4328378 c.-905G>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0