TB-Profiler result

Run: ERR9786554
Summary

Run ID: ERR9786554

Sample name:

Date: 02-04-2023 12:31:40

Number of reads: 978187

Percentage reads mapped: 99.53

Strain: lineage4.6.2.2;lineage4.1.1.3;lineage1.1.1

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 0.94
lineage1 Indo-Oceanic EAI RD239 0.05
lineage4.6 Euro-American T;LAM None 0.78
lineage4.1 Euro-American T;X;H None 0.1
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.12
lineage4.6.2 Euro-American T;LAM RD726 0.73
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.08
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.07
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 0.76
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.09
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 6112 p.Met291Ile missense_variant 0.12
gyrA 6439 c.-863C>G upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 0.14
rpoC 763884 p.Ala172Val missense_variant 0.18
rpoC 763886 c.517C>A synonymous_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.2
mmpR5 778298 c.-692C>T upstream_gene_variant 0.65
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473791 n.134A>G non_coding_transcript_exon_variant 0.18
rpsA 1833727 c.186G>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 0.77
PPE35 2167926 p.Leu896Ser missense_variant 0.27
PPE35 2167983 p.Gly877Asp missense_variant 0.26
PPE35 2169829 p.Ala262Thr missense_variant 0.17
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.81
Rv1979c 2222308 p.Asp286Gly missense_variant 0.11
Rv1979c 2223124 p.Leu14Arg missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290214 c.-973T>C upstream_gene_variant 0.1
kasA 2518132 c.18C>T synonymous_variant 0.17
thyX 3067430 c.516C>A synonymous_variant 0.12
thyX 3067433 c.513C>G synonymous_variant 0.12
thyX 3067439 c.507A>G synonymous_variant 0.12
thyX 3067474 p.Pro158Ala missense_variant 0.71
ald 3086788 c.-32T>C upstream_gene_variant 0.26
Rv3083 3448567 p.His22Asp missense_variant 0.71
Rv3083 3448714 p.Asp71His missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474342 c.336G>A synonymous_variant 0.16
fprA 3474597 c.591C>A synonymous_variant 0.13
Rv3236c 3612571 c.546C>T synonymous_variant 0.77
embC 4241042 p.Asn394Asp missense_variant 0.17
embA 4242550 c.-683C>G upstream_gene_variant 0.75
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245745 p.Pro838Leu missense_variant 0.52
embA 4245969 p.Pro913Ser missense_variant 0.14
embB 4249408 c.2895G>A synonymous_variant 0.16
aftB 4267272 p.Lys522Arg missense_variant 0.82
ubiA 4269387 p.Glu149Asp missense_variant 0.13
ethR 4326739 c.-810G>C upstream_gene_variant 0.7
ethA 4328004 c.-531C>T upstream_gene_variant 0.69
whiB6 4338314 p.Ala70Thr missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.13