TB-Profiler result

Run: ERR2229042
Summary

Run ID: ERR2229042

Sample name:

Date: 31-03-2023 16:33:46

Number of reads: 1200818

Percentage reads mapped: 98.97

Strain: lineage4.8

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
lineage4.8 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
katG 2155137 c.974delC frameshift_variant 0.11 isoniazid, 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
ccsA 620667 p.Trp259* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.25
mmpL5 777122 c.1359C>T synonymous_variant 0.22
mmpL5 777128 c.1353A>G synonymous_variant 0.2
mmpL5 777136 p.Met449Leu missense_variant 0.18
mmpL5 777173 c.1308C>T synonymous_variant 0.15
mmpL5 777176 p.Glu435Asp missense_variant 0.15
mmpL5 777191 c.1290C>A synonymous_variant 0.18
mmpL5 777196 p.Glu429Gln missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304333 p.Ser468Asn missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.13
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
fabG1 1673491 p.Val18Ile missense_variant 0.13
rpsA 1834421 p.Gly294Trp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102450 p.Lys198Met missense_variant 0.16
PPE35 2168140 p.Ala825Thr missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518409 p.Gly99Cys missense_variant 0.14
kasA 2518933 c.819C>T synonymous_variant 0.15
Rv2752c 3065823 c.369G>A synonymous_variant 0.12
Rv2752c 3066159 c.33G>A synonymous_variant 0.13
fbiD 3339486 c.369G>A synonymous_variant 0.13
fprA 3474144 p.Trp46Cys missense_variant 0.17
fprA 3474529 p.Arg175Cys missense_variant 0.12
rpoA 3877467 c.1041T>C synonymous_variant 0.13
clpC1 4038220 p.Glu829Lys missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.24
embB 4246548 p.Pro12Gln missense_variant 0.27
embB 4246555 c.42G>C synonymous_variant 0.31
embB 4246556 p.Ala15Pro missense_variant 0.31
embB 4246747 p.Asp78Glu missense_variant 0.29
aftB 4269201 c.-365A>G upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0