TB-Profiler result

Run: ERR9786699
Summary

Run ID: ERR9786699

Sample name:

Date: 02-04-2023 12:40:15

Number of reads: 1634233

Percentage reads mapped: 99.62

Strain: lineage6.1.1;lineage4.1.2.1

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 0.77
lineage6 West-Africa 2 AFRI_1 RD702 0.24
lineage4.1 Euro-American T;X;H None 0.75
lineage6.1.1 West-Africa 2 AFRI_1 RD702 0.13
lineage4.1.2 Euro-American T;H None 0.78
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.77
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 6446 p.Ala403Ser missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8493 p.Leu398Phe missense_variant 0.22
gyrA 9143 c.1842T>C synonymous_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491256 p.Lys158Asn missense_variant 0.73
fgd1 491591 p.Lys270Met missense_variant 0.82
fgd1 491668 p.Lys296Glu missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 0.24
mshA 575679 p.Asn111Ser missense_variant 0.83
rpoB 760115 c.309C>T synonymous_variant 0.73
rpoB 760855 p.Thr350Ile missense_variant 0.33
rpoB 760969 p.Ser388Leu missense_variant 0.25
rpoB 761723 p.Glu639Asp missense_variant 0.28
rpoC 763031 c.-339T>C upstream_gene_variant 0.24
rpoC 765150 p.Gly594Glu missense_variant 0.79
rpoC 766231 c.2862T>C synonymous_variant 0.21
rpoC 767227 c.3858G>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.18
Rv1258c 1406341 p.Tyr334His missense_variant 0.73
Rv1258c 1406685 p.Val219Ala missense_variant 0.28
embR 1416633 p.Leu239Val missense_variant 0.23
atpE 1461251 c.207G>T synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674434 p.Val78Ala missense_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.14
katG 2155503 c.609C>T synonymous_variant 0.16
PPE35 2167926 p.Leu896Ser missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.82
kasA 2518132 c.18C>T synonymous_variant 0.23
Rv2752c 3064876 p.Ser439Phe missense_variant 0.7
ald 3086728 c.-92C>T upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
fprA 3475159 p.Asn385Asp missense_variant 0.3
Rv3236c 3612143 p.Arg325His missense_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 0.2
embC 4241843 p.Leu661Ile missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.82
embA 4244220 c.988C>T synonymous_variant 0.16
embA 4244379 p.Pro383Ser missense_variant 0.17
embB 4246864 c.351C>T synonymous_variant 0.2
embB 4248585 p.Arg691Leu missense_variant 0.83
aftB 4269351 c.-515C>T upstream_gene_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 0.15
aftB 4269522 c.-686C>T upstream_gene_variant 0.15
aftB 4269606 c.-770T>C upstream_gene_variant 0.11
ethA 4326465 p.Ile337Val missense_variant 0.23
ethA 4326644 p.Asp277Gly missense_variant 0.77
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.23
gid 4408034 p.Glu57Lys missense_variant 0.26