TB-Profiler result

Run: ERR1950065
Summary

Run ID: ERR1950065

Sample name:

Date: 31-03-2023 15:38:52

Number of reads: 834023

Percentage reads mapped: 99.54

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 0.99
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
gyrB 6971 p.Pro578Thr missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7666 p.Asp122Ala missense_variant 0.18
gyrA 8881 p.Lys527Arg missense_variant 0.11
fgd1 491184 p.Glu134Asp missense_variant 0.17
fgd1 491445 c.663C>T synonymous_variant 0.25
fgd1 491489 p.Asp236Ala missense_variant 0.25
fgd1 491508 c.726A>G synonymous_variant 0.15
ccsA 619787 c.-104T>G upstream_gene_variant 0.2
ccsA 620117 p.Val76Gly missense_variant 0.25
rpoC 764388 p.Leu340Ser missense_variant 0.12
rpoC 765598 p.Lys743Asn missense_variant 0.18
rpoC 765753 p.Asp795Val missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775699 p.Ser928Ala missense_variant 0.22
mmpL5 775962 p.Val840Gly missense_variant 0.18
mmpL5 776204 c.2277C>T synonymous_variant 0.17
mmpS5 778575 p.Ser111Pro missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304984 p.Leu685Arg missense_variant 0.17
atpE 1461223 p.Val60Ala missense_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471799 n.-47A>T upstream_gene_variant 0.25
rrs 1472513 n.668T>A non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475050 n.1393A>T non_coding_transcript_exon_variant 0.38
rrl 1475472 n.1815T>A non_coding_transcript_exon_variant 0.22
inhA 1674586 p.Ser129Pro missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167679 c.2934G>T synonymous_variant 0.18
PPE35 2168133 p.Asp827Ala missense_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168876 p.Phe579Leu missense_variant 0.38
PPE35 2169006 p.Ser536* stop_gained 0.25
PPE35 2169031 p.Asp528Tyr missense_variant 0.22
PPE35 2169790 p.Leu275Met missense_variant 0.33
PPE35 2169918 p.Leu232His missense_variant 0.4
PPE35 2170308 p.Leu102Pro missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223353 c.-189T>C upstream_gene_variant 0.13
pncA 2289193 p.Gly17Arg missense_variant 0.11
kasA 2518449 p.Val112Gly missense_variant 0.25
kasA 2518845 p.Ala244Glu missense_variant 0.17
folC 2747765 c.-167A>T upstream_gene_variant 0.22
ribD 2986960 p.Leu41Trp missense_variant 0.4
Rv2752c 3065629 p.Met188Thr missense_variant 0.23
Rv2752c 3067009 c.-818A>C upstream_gene_variant 0.33
thyA 3074318 p.Phe52Ile missense_variant 0.22
ald 3086705 c.-115T>A upstream_gene_variant 0.33
fprA 3474247 p.Asn81Tyr missense_variant 0.36
Rv3236c 3612164 p.Val318Ala missense_variant 0.27
Rv3236c 3612952 c.165T>G synonymous_variant 0.14
fbiA 3640541 c.-2A>T upstream_gene_variant 0.22
fbiB 3641953 p.Leu140Arg missense_variant 0.25
fbiB 3642827 p.Glu431Asp missense_variant 0.15
clpC1 4038538 p.Thr723Pro missense_variant 0.29
clpC1 4038849 p.Phe619Cys missense_variant 0.67
panD 4044477 c.-196T>G upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244205 p.Arg325Cys missense_variant 0.13
embA 4244842 p.Arg537Gln missense_variant 0.2
embA 4244871 p.Gly547Ser missense_variant 0.18
embB 4247126 p.Thr205Ala missense_variant 0.33
embB 4247133 p.Asp207Ala missense_variant 0.29
embB 4248743 p.Val744Ile missense_variant 0.15
embB 4249700 p.Ser1063Pro missense_variant 0.13
ethA 4326152 p.Arg441His missense_variant 0.17
ethA 4326409 c.1065T>A synonymous_variant 0.22
ethA 4326434 p.Gln347Leu missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0