TB-Profiler result

Run: ERR2229439
Summary

Run ID: ERR2229439

Sample name:

Date: 31-03-2023 17:11:40

Number of reads: 668621

Percentage reads mapped: 99.41

Strain: lineage4.8

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
lineage4.8 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
folC 2747141 p.Glu153Gly missense_variant 0.15 para-aminosalicylic_acid
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 7881 p.Leu194Met missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.27
ccsA 619917 c.27C>A synonymous_variant 0.11
rpoC 765705 p.Lys779Arg missense_variant 0.22
rpoC 766846 c.3477C>T synonymous_variant 0.22
rpoC 767002 c.3633G>A synonymous_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800641 c.-168_-167insC upstream_gene_variant 0.18
rplC 800854 p.Val16Ile missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304616 p.Cys562* stop_gained 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473171 n.1326G>C non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475459 n.1804delA non_coding_transcript_exon_variant 0.22
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.12
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.13
rrl 1476683 n.3026T>A non_coding_transcript_exon_variant 0.25
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.17
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
inhA 1674342 c.141T>A synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102635 c.408C>T synonymous_variant 0.13
katG 2155234 p.Leu293Arg missense_variant 0.17
katG 2156434 c.-323G>A upstream_gene_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.24
PPE35 2170147 p.Ser156Ala missense_variant 0.15
PPE35 2170157 p.Ala152Ser missense_variant 0.5
PPE35 2170232 c.381T>C synonymous_variant 0.13
PPE35 2170235 c.378T>C synonymous_variant 0.13
PPE35 2170238 c.375T>G synonymous_variant 0.13
Rv1979c 2223140 p.Tyr9His missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289146 p.Ser32Arg missense_variant 0.11
kasA 2519317 c.1203G>T synonymous_variant 0.18
folC 2746182 p.Val473Ile missense_variant 0.18
folC 2746340 p.Ala420Glu missense_variant 0.2
folC 2746714 c.885T>C synonymous_variant 0.15
folC 2747322 p.Thr93Ser missense_variant 0.33
pepQ 2859638 c.781C>A synonymous_variant 0.15
pepQ 2860343 p.Asp26Asn missense_variant 0.12
Rv2752c 3066159 c.33G>T synonymous_variant 0.4
thyX 3067409 c.537C>A synonymous_variant 0.17
thyA 3074574 c.-103G>A upstream_gene_variant 0.15
fbiD 3339364 p.Pro83Ala missense_variant 0.14
fprA 3474654 c.648C>T synonymous_variant 0.17
fprA 3475259 p.Val418Ala missense_variant 0.13
Rv3236c 3612206 p.Thr304Ile missense_variant 0.13
alr 3840671 c.750G>T synonymous_variant 0.11
clpC1 4039444 p.Leu421Ile missense_variant 0.2
clpC1 4039645 p.His354Asp missense_variant 0.1
clpC1 4039829 p.Leu292Phe missense_variant 0.13
panD 4044159 c.123C>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267965 p.Arg291Leu missense_variant 0.18
ethA 4326255 p.Asn407Tyr missense_variant 0.13
ethA 4328385 c.-912G>C upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0