TB-Profiler result

Run: ERR751293
Summary

Run ID: ERR751293

Sample name:

Date: 19-10-2023 20:29:46

Number of reads: 4631321

Percentage reads mapped: 98.91

Strain: lineage6.3.1;lineage5.1.2

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
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 0.4
lineage6 West-Africa 2 AFRI_1 RD702 0.66
lineage6.3 West-Africa 2 AFRI_1 RD702 0.65
lineage5.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.29
lineage5.1.2 West-Africa 1 AFRI_2;AFRI_3 RD711 0.24
lineage6.3.1 West-Africa 2 AFRI_1 RD702 0.65
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 1.0
gyrA 7362 p.Glu21Gln missense_variant 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 0.33
fgd1 491668 p.Lys296Glu missense_variant 0.77
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760969 p.Ser388Leu missense_variant 0.66
rpoB 761723 p.Glu639Asp missense_variant 0.57
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1407273 p.Asp23Val missense_variant 0.34
atpE 1461251 c.207G>T synonymous_variant 0.76
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673338 c.-864G>A upstream_gene_variant 0.39
inhA 1674434 p.Val78Ala missense_variant 0.62
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918692 c.753G>A synonymous_variant 0.63
ndh 2101921 c.1122G>A synonymous_variant 0.41
ndh 2102694 p.Val117Ile missense_variant 0.74
ndh 2103112 c.-70G>T upstream_gene_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 0.65
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170265 c.347delG frameshift_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222852 p.Ala105Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290062 c.-821G>A upstream_gene_variant 0.32
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726261 c.69G>T synonymous_variant 0.15
ald 3086728 c.-92C>T upstream_gene_variant 0.7
ald 3086788 c.-32T>C upstream_gene_variant 0.71
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 0.3
Rv3083 3449644 p.Ala381Thr missense_variant 0.27
Rv3083 3449781 c.1278G>A synonymous_variant 0.64
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3840932 c.489C>T synonymous_variant 0.38
rpoA 3877696 p.Thr271Ile missense_variant 0.73
rpoA 3878493 c.15G>A synonymous_variant 0.33
ddn 3986987 c.144G>T synonymous_variant 0.25
ddn 3987180 p.Asp113Asn missense_variant 0.36
clpC1 4040824 c.-120C>T upstream_gene_variant 0.24
embC 4239843 c.-20A>C upstream_gene_variant 0.37
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241843 p.Leu661Ile missense_variant 0.68
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244379 p.Pro383Ser missense_variant 0.62
embA 4244635 p.Val468Ala missense_variant 0.38
embA 4245147 p.Pro639Ser missense_variant 0.27
embB 4246864 c.351C>T synonymous_variant 0.72
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268477 c.360C>T synonymous_variant 0.45
aftB 4269351 c.-515C>T upstream_gene_variant 0.67
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269522 c.-686C>T upstream_gene_variant 0.52
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326465 p.Ile337Val missense_variant 0.64
ethR 4326928 c.-621G>A upstream_gene_variant 0.38
ethA 4327103 p.Gly124Asp missense_variant 0.3
whiB6 4338547 c.-26A>G upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0