TB-Profiler result

Run: ERR2229447
Summary

Run ID: ERR2229447

Sample name:

Date: 31-03-2023 17:12:04

Number of reads: 523769

Percentage reads mapped: 99.4

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 7362 p.Glu21Gln missense_variant 1.0
fgd1 490605 c.-178G>T upstream_gene_variant 0.2
rpoB 759770 c.-37C>A upstream_gene_variant 0.11
rpoC 764949 p.Leu527* stop_gained 0.17
rpoC 765755 p.Asp796Asn missense_variant 0.18
rpoC 766073 p.Ala902Thr missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.15
mmpL5 776021 c.2460G>C synonymous_variant 0.15
mmpL5 776210 p.Tyr757* stop_gained 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781583 c.24C>A synonymous_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304330 p.Ala467Asp missense_variant 0.22
fbiC 1305010 p.Val694Met missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475573 n.1921delC non_coding_transcript_exon_variant 0.12
rrl 1476601 n.2944G>T non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102348 p.Ala232Glu missense_variant 0.17
ndh 2102685 p.Gly120Ser missense_variant 0.13
katG 2156151 c.-40T>A upstream_gene_variant 0.18
katG 2156221 c.-110C>A upstream_gene_variant 0.18
PPE35 2167745 p.Thr956Arg missense_variant 0.21
PPE35 2167865 c.2748G>C synonymous_variant 0.23
PPE35 2167868 c.2745A>C synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169879 p.Phe245Ser missense_variant 0.11
PPE35 2169890 c.723C>T synonymous_variant 0.13
PPE35 2169893 c.720C>A synonymous_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2169910 p.Asn235Tyr missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170053 p.Thr187Ser missense_variant 0.13
PPE35 2170392 p.Gly74Ala missense_variant 0.15
PPE35 2170400 c.213G>C synonymous_variant 0.15
PPE35 2170415 c.198A>G synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289037 p.Pro69Thr missense_variant 0.12
kasA 2518723 p.Glu203Asp missense_variant 0.5
eis 2715483 c.-151C>A upstream_gene_variant 0.13
folC 2746367 c.1231delG frameshift_variant 0.25
Rv2752c 3064745 p.Thr483Ser missense_variant 0.18
Rv2752c 3064773 c.1419C>T synonymous_variant 0.12
thyA 3074038 p.Pro145Leu missense_variant 0.18
thyA 3074392 p.Arg27His missense_variant 0.22
fprA 3473978 c.-29G>T upstream_gene_variant 0.13
Rv3236c 3613294 c.-178G>A upstream_gene_variant 0.17
clpC1 4038716 c.1989C>T synonymous_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.22
panD 4044253 p.Ile10Asn missense_variant 0.4
embC 4240060 c.198G>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245711 p.Ala827Ser missense_variant 0.29
embB 4248552 p.Ala680Asp missense_variant 0.17
aftB 4267029 p.Asp603Val missense_variant 0.17
aftB 4267634 c.1203G>T synonymous_variant 0.22
whiB6 4338352 p.Pro57Gln missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407604 p.Ala200Val missense_variant 0.15
gid 4407849 c.354C>A synonymous_variant 0.14
gid 4408474 c.-272A>T upstream_gene_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0