TB-Profiler result

Run: ERR2229062
Summary

Run ID: ERR2229062

Sample name:

Date: 31-03-2023 16:34:29

Number of reads: 521880

Percentage reads mapped: 99.4

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 2155105 c.1006delC frameshift_variant 0.14 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
rpoB 760008 p.Ala68Ser missense_variant 0.12
rpoB 760606 p.Ala267Glu missense_variant 0.22
rpoB 761850 p.Pro682Ser missense_variant 0.14
rpoC 763702 c.333C>A synonymous_variant 0.2
rpoC 766753 c.3384C>T synonymous_variant 0.17
rpoC 766826 p.His1153Asn missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775685 c.2796C>A synonymous_variant 0.4
mmpL5 775688 c.2793C>A synonymous_variant 0.33
mmpL5 775691 c.2790G>C synonymous_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
atpE 1461224 c.180T>C synonymous_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471787 n.-59T>C upstream_gene_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476454 n.2797C>T non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
rpsA 1834027 c.486G>A synonymous_variant 0.13
rpsA 1834550 p.Val337Met missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154345 c.1767C>T synonymous_variant 0.15
katG 2156085 c.27A>G synonymous_variant 0.13
PPE35 2168014 p.Ala867Ser missense_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169287 c.1326T>C synonymous_variant 0.11
PPE35 2169293 c.1320T>C synonymous_variant 0.11
PPE35 2169337 p.Asp426His missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.36
PPE35 2170235 c.378T>C synonymous_variant 0.1
PPE35 2170238 c.375T>G synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289749 c.-508G>T upstream_gene_variant 0.29
ribD 2987487 p.Pro217Ser missense_variant 0.17
thyX 3067736 p.Phe70Leu missense_variant 0.29
ald 3087467 p.His216Gln missense_variant 0.13
Rv3083 3448405 c.-99G>A upstream_gene_variant 0.29
fprA 3473808 c.-199C>A upstream_gene_variant 0.12
fprA 3474435 c.429C>A synonymous_variant 0.15
Rv3236c 3612084 p.Gly345Arg missense_variant 0.12
Rv3236c 3612288 p.Gly277Arg missense_variant 0.18
fbiA 3641128 p.Ala196Ser missense_variant 0.14
alr 3840888 p.Ala178Glu missense_variant 0.15
rpoA 3878315 p.Thr65Ala missense_variant 0.12
rpoA 3878366 p.Gly48* stop_gained 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.11
clpC1 4040328 p.Lys126Arg missense_variant 0.15
panD 4043907 c.375C>A synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243629 p.Ala133Ser missense_variant 0.22
embA 4245380 p.Tyr716* stop_gained 0.18
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4247059 c.546C>G synonymous_variant 0.18
embB 4247060 p.Pro183Ala missense_variant 0.18
embB 4247066 p.Ile185Val missense_variant 0.18
embB 4248778 c.2265C>G synonymous_variant 0.13
embB 4249676 p.Arg1055Ser missense_variant 0.22
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethA 4327297 p.Met59Ile missense_variant 0.17
ethA 4327938 c.-465G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0