TB-Profiler result

Run: ERR4819152

Summary

Run ID: ERR4819152

Sample name:

Date: 01-04-2023 15:57:02

Number of reads: 744119

Percentage reads mapped: 99.78

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 5452 p.Glu71Asp missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7655 c.354G>T synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9411 c.2110C>A synonymous_variant 0.11
fgd1 490647 c.-136C>T upstream_gene_variant 0.11
fgd1 491311 p.Gly177Ser missense_variant 0.14
mshA 576759 p.His471Arg missense_variant 0.12
rpoB 760799 p.Asp331Glu missense_variant 0.15
rpoB 761585 c.1779C>T synonymous_variant 0.13
rpoB 761945 c.2139G>C synonymous_variant 0.12
rpoC 763166 c.-204A>G upstream_gene_variant 0.13
rpoC 763530 p.Pro54Leu missense_variant 0.18
rpoC 765371 c.2002C>T synonymous_variant 0.12
rpoC 765686 p.Ala773Pro missense_variant 0.17
rpoC 766051 p.Glu894Asp missense_variant 0.17
rpoC 766374 p.Ser1002Tyr missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777149 c.1332C>T synonymous_variant 0.12
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
mmpL5 779076 c.-596G>T upstream_gene_variant 0.14
mmpL5 779094 c.-614C>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303875 c.945G>A synonymous_variant 0.14
fbiC 1305317 p.Thr796Ile missense_variant 0.14
Rv1258c 1407068 c.273G>C synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471660 n.-185delC upstream_gene_variant 0.12
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.33
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918023 c.84C>T synonymous_variant 0.13
ndh 2102517 p.Val176Phe missense_variant 0.12
katG 2155389 c.723C>G synonymous_variant 1.0
katG 2156519 c.-408T>C upstream_gene_variant 0.11
PPE35 2169191 c.1422G>A synonymous_variant 0.29
PPE35 2170394 c.219G>C synonymous_variant 0.11
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.92
Rv1979c 2221845 c.1320G>T synonymous_variant 0.15
Rv1979c 2221922 p.Lys415Glu missense_variant 0.13
Rv1979c 2221956 c.1209A>G synonymous_variant 0.11
Rv1979c 2223065 c.100C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290129 c.-890_-889delGC upstream_gene_variant 0.18
kasA 2517980 c.-135C>A upstream_gene_variant 0.18
eis 2714161 p.Ala391Val missense_variant 0.2
eis 2714692 p.Ser214* stop_gained 0.12
folC 2746243 c.1356C>T synonymous_variant 0.15
folC 2747721 c.-123C>G upstream_gene_variant 0.18
Rv2752c 3065022 c.1170G>A synonymous_variant 0.12
Rv2752c 3067124 c.-933G>A upstream_gene_variant 0.18
thyX 3067474 p.Pro158Ala missense_variant 1.0
ald 3086864 c.45G>A synonymous_variant 0.12
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3448843 p.Cys114Arg missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474453 c.447G>A synonymous_variant 0.12
fprA 3475077 c.1071C>T synonymous_variant 0.18
whiB7 3568792 c.-113C>A upstream_gene_variant 0.14
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
Rv3236c 3613070 p.Ala16Val missense_variant 0.11
fbiA 3640510 c.-33G>A upstream_gene_variant 0.14
clpC1 4040793 c.-89G>A upstream_gene_variant 0.13
panD 4043967 c.315C>T synonymous_variant 0.13
embC 4240552 c.690G>A synonymous_variant 0.11
embC 4241135 p.Val425Leu missense_variant 0.14
embC 4242035 p.Gln725Glu missense_variant 0.2
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244882 p.Trp550Cys missense_variant 0.25
embA 4245149 c.1917C>T synonymous_variant 0.11
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4268284 p.Val185Leu missense_variant 0.12
aftB 4268562 p.Leu92Pro missense_variant 0.17
ubiA 4269477 p.Met119Ile missense_variant 0.12
ubiA 4269488 p.Gly116Ser missense_variant 0.11
ubiA 4269985 c.-152T>C upstream_gene_variant 0.1
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethR 4327961 p.Trp138Leu missense_variant 0.25
ethR 4327983 p.Trp145* stop_gained 0.15
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338582 c.-61G>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0