TB-Profiler result

Run: ERR2229429
Summary

Run ID: ERR2229429

Sample name:

Date: 31-03-2023 17:10:48

Number of reads: 351914

Percentage reads mapped: 99.41

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 2154859 p.Arg418Gln missense_variant 0.29 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
gyrA 8689 p.Ala463Val missense_variant 0.25
gyrA 9666 p.Arg789Ser missense_variant 0.17
rpoB 759670 c.-137C>T upstream_gene_variant 0.2
rpoB 761084 c.1278C>A synonymous_variant 0.25
rpoC 765075 p.Ala569Val missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777246 p.Arg412Gln missense_variant 0.4
mmpL5 777499 p.Arg328Gly missense_variant 0.25
mmpL5 778933 c.-453G>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781692 p.Pro45Ser missense_variant 0.29
fbiC 1303343 p.Phe138Ser missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304490 c.1560C>T synonymous_variant 0.33
fbiC 1304578 p.Arg550Gly missense_variant 0.33
embR 1417271 p.Thr26Ile missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472125 n.280G>A non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.2
fabG1 1673359 c.-81T>C upstream_gene_variant 0.21
fabG1 1673361 c.-79C>G upstream_gene_variant 0.21
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102401 c.642T>C synonymous_variant 0.17
katG 2156362 c.-251C>A upstream_gene_variant 0.13
PPE35 2167745 p.Thr956Arg missense_variant 0.17
PPE35 2167865 c.2748G>C synonymous_variant 0.22
PPE35 2167868 c.2745A>C synonymous_variant 0.2
PPE35 2168568 p.Thr682Lys missense_variant 0.12
PPE35 2168640 p.Ile658Thr missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169044 c.1569G>C synonymous_variant 0.25
PPE35 2169145 p.Val490Leu missense_variant 0.17
PPE35 2169365 p.Ser416Asn missense_variant 0.18
PPE35 2169488 c.1125G>C synonymous_variant 0.15
PPE35 2169491 c.1122T>C synonymous_variant 0.15
PPE35 2169581 c.1032C>G synonymous_variant 0.12
PPE35 2169587 c.1026G>A synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.15
PPE35 2170159 p.Ala152Ser missense_variant 0.13
PPE35 2170463 c.150C>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289967 c.-726C>T upstream_gene_variant 0.2
pncA 2289993 c.-752C>T upstream_gene_variant 0.2
kasA 2518064 c.-51G>T upstream_gene_variant 0.17
ahpC 2726591 c.399C>A synonymous_variant 0.12
Rv2752c 3064908 c.1284C>T synonymous_variant 0.2
Rv2752c 3066132 c.60G>T synonymous_variant 0.29
thyA 3073919 p.Thr185Pro missense_variant 0.25
ald 3086644 c.-176G>A upstream_gene_variant 0.2
ald 3086765 c.-55G>T upstream_gene_variant 0.13
fprA 3475230 p.Asp408Glu missense_variant 0.4
fprA 3475297 c.1291C>A synonymous_variant 0.25
Rv3236c 3612324 p.Pro265Thr missense_variant 0.18
fbiB 3640558 c.-977C>T upstream_gene_variant 0.25
alr 3841416 p.Lys2Ile missense_variant 0.22
rpoA 3878189 p.Ala107Thr missense_variant 0.13
ddn 3986814 c.-30T>A upstream_gene_variant 0.12
clpC1 4038752 c.1953G>A synonymous_variant 0.18
clpC1 4040402 p.Asn101Lys missense_variant 0.2
panD 4044208 p.Ser25* stop_gained 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.33
embB 4249279 c.2766C>T synonymous_variant 0.17
aftB 4266991 p.Asp616Tyr missense_variant 0.22
aftB 4267280 p.Glu519Asp missense_variant 0.2
aftB 4267310 c.1527G>C synonymous_variant 0.18
ubiA 4269430 p.Gln135Arg missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407982 p.Leu74Ser missense_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0