TB-Profiler result

Run: ERR2229317
Summary

Run ID: ERR2229317

Sample name:

Date: 31-03-2023 17:01:39

Number of reads: 1280989

Percentage reads mapped: 98.48

Strain: lineage4.8

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 2155627 c.484delG frameshift_variant 0.14 isoniazid
katG 2155647 p.Tyr155* stop_gained 0.13 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
fgd1 491407 p.Pro209Thr missense_variant 0.4
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576289 c.942G>C synonymous_variant 0.22
ccsA 620795 p.Ala302Val missense_variant 0.12
rpoC 765517 c.2148C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775850 p.Ser877Arg missense_variant 0.25
mmpL5 777176 p.Glu435Asp missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1417340 p.Gly3Val missense_variant 0.13
embR 1417358 c.-11G>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472694 n.849C>A non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475674 n.2017A>G non_coding_transcript_exon_variant 0.11
rrl 1476627 n.2970G>A non_coding_transcript_exon_variant 0.17
rrl 1476667 n.3010T>A non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.34
fabG1 1673862 c.424delT frameshift_variant 0.17
rpsA 1834450 p.Lys303Asn missense_variant 0.25
rpsA 1834851 p.Ala437Val missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.2
PPE35 2167762 p.Ser951Pro missense_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.15
PPE35 2168047 p.Leu856Val missense_variant 0.11
PPE35 2168235 p.Ala793Glu missense_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169717 p.Asn299Ile missense_variant 0.12
PPE35 2169725 c.888T>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.64
PPE35 2170053 p.Thr187Ser missense_variant 0.65
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518209 p.Thr32Lys missense_variant 0.12
ribD 2987006 c.170delG frameshift_variant 0.33
Rv2752c 3064795 p.Leu466Pro missense_variant 0.14
thyX 3068015 c.-70T>G upstream_gene_variant 0.11
fbiD 3339736 p.Thr207Pro missense_variant 0.18
Rv3236c 3612997 c.120T>C synonymous_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.15
clpC1 4039018 p.Ser563Ala missense_variant 0.11
panD 4044395 c.-114C>A upstream_gene_variant 0.14
panD 4044404 c.-123G>A upstream_gene_variant 0.13
embC 4241616 p.Lys585Arg missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244665 p.Thr478Arg missense_variant 0.14
embA 4244720 c.1488C>T synonymous_variant 0.15
embA 4244918 c.1686G>T synonymous_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.19
embB 4246548 p.Pro12Gln missense_variant 0.44
embB 4246555 c.42G>C synonymous_variant 0.46
embB 4246556 p.Ala15Pro missense_variant 0.46
embB 4246563 p.Leu17Trp missense_variant 0.21
ubiA 4269479 p.Met119Leu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0