TB-Profiler result

Run: ERR751349
Summary

Run ID: ERR751349

Sample name:

Date: 19-10-2023 20:34:46

Number of reads: 4782857

Percentage reads mapped: 99.55

Strain: lineage5.1.1;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
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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 0.73
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 0.33
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.68
lineage5.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.29
lineage5.1.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.3
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 0.44
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.32
gyrA 9143 c.1842T>C synonymous_variant 0.31
gyrA 9304 p.Gly668Asp missense_variant 0.25
gyrA 9566 c.2265C>T synonymous_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 0.38
rpoC 763031 c.-339T>C upstream_gene_variant 0.27
rpoC 763280 c.-90C>T upstream_gene_variant 0.26
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.24
Rv1258c 1407273 p.Asp23Val missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673338 c.-864G>A upstream_gene_variant 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101840 c.1203G>A synonymous_variant 0.29
ndh 2101921 c.1122G>A synonymous_variant 0.29
ndh 2103112 c.-70G>T upstream_gene_variant 0.27
katG 2154724 p.Arg463Leu missense_variant 0.28
PPE35 2167926 p.Leu896Ser missense_variant 0.28
PPE35 2168149 p.Pro822Ser missense_variant 0.68
Rv1979c 2222569 p.Ala199Val missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
pncA 2290062 c.-821G>A upstream_gene_variant 0.29
kasA 2518132 c.18C>T synonymous_variant 0.31
ald 3087084 c.266delA frameshift_variant 0.27
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 0.25
Rv3083 3449644 p.Ala381Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.31
fprA 3475159 p.Asn385Asp missense_variant 0.32
alr 3840932 c.489C>T synonymous_variant 0.38
rpoA 3878493 c.15G>A synonymous_variant 0.3
ddn 3986987 c.144G>T synonymous_variant 0.3
ddn 3987180 p.Asp113Asn missense_variant 0.33
clpC1 4039729 p.Asp326Asn missense_variant 0.76
clpC1 4040824 c.-120C>T upstream_gene_variant 0.39
embC 4239843 c.-20A>C upstream_gene_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 0.26
embA 4244635 p.Val468Ala missense_variant 0.35
embA 4245147 p.Pro639Ser missense_variant 0.34
embB 4247646 p.Glu378Ala missense_variant 0.28
ubiA 4269387 p.Glu149Asp missense_variant 0.28
aftB 4269606 c.-770T>C upstream_gene_variant 0.3
aftB 4269768 c.-932C>A upstream_gene_variant 0.22
ethR 4326928 c.-621G>A upstream_gene_variant 0.32
ethA 4327103 p.Gly124Asp missense_variant 0.35
whiB6 4338547 c.-26A>G upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.34