TB-Profiler result

Run: ERR4796787
Summary

Run ID: ERR4796787

Sample name:

Date: 20-10-2023 01:56:39

Number of reads: 5426414

Percentage reads mapped: 99.61

Strain: lineage4.4.1.1;lineage3;lineage1.2.2.2

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.44)
Isoniazid R katG p.Ser315Thr (0.53), ahpC p.Glu76Lys (0.36)
Ethambutol R embB p.Met306Ile (0.48)
Pyrazinamide R pncA p.Ser104Arg (0.62)
Streptomycin R gid c.102delG (0.57)
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
lineage3 East-African-Indian CAS RD750 0.14
lineage4 Euro-American LAM;T;S;X;H None 0.48
lineage1 Indo-Oceanic EAI RD239 0.37
lineage4.4 Euro-American S;T None 0.52
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.33
lineage4.4.1 Euro-American (S-type) S;T None 0.55
lineage1.2.2.2 Indo-Oceanic NA RD239 0.32
lineage4.4.1.1 Euro-American S;Orphans None 0.53
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
rpoB 761155 p.Ser450Leu missense_variant 0.44 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.53 isoniazid
pncA 2288932 p.Ser104Arg missense_variant 0.62 pyrazinamide
ahpC 2726418 p.Glu76Lys missense_variant 0.36 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.48 ethambutol
gid 4408100 c.102delG frameshift_variant 0.57 streptomycin
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 5075 c.-165C>T upstream_gene_variant 0.36
gyrB 6112 p.Met291Ile missense_variant 0.36
gyrA 7268 c.-34C>T upstream_gene_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.98
gyrA 8452 p.Ala384Val missense_variant 0.24
gyrA 9143 c.1842T>C synonymous_variant 0.27
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.37
rpoB 759939 p.Pro45Ser missense_variant 0.42
rpoB 762167 c.2361T>C synonymous_variant 0.6
rpoC 763031 c.-339T>C upstream_gene_variant 0.48
rpoC 763884 p.Ala172Val missense_variant 0.29
rpoC 763886 c.517C>A synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775750 p.Gly911Ser missense_variant 0.45
mmpL5 776100 p.Thr794Ile missense_variant 0.53
mmpS5 779625 c.-720G>A upstream_gene_variant 0.28
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416814 c.534G>A synonymous_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473021 n.1176G>A non_coding_transcript_exon_variant 0.33
inhA 1673658 c.-544G>A upstream_gene_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.41
ndh 2102990 p.Val18Ala missense_variant 0.48
katG 2154345 c.1767C>A synonymous_variant 0.58
katG 2154724 p.Arg463Leu missense_variant 0.51
PPE35 2167926 p.Leu896Ser missense_variant 0.42
PPE35 2168742 p.Gly624Asp missense_variant 0.39
PPE35 2169840 p.Gly258Asp missense_variant 0.56
Rv1979c 2222308 p.Asp286Gly missense_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 0.25
ahpC 2726051 c.-142G>A upstream_gene_variant 0.35
ahpC 2726105 c.-88G>A upstream_gene_variant 0.13
thyX 3067949 c.-4C>T upstream_gene_variant 0.47
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.53
Rv3083 3448714 p.Asp71His missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.32
fprA 3475159 p.Asn385Asp missense_variant 0.32
whiB7 3568857 c.-178C>T upstream_gene_variant 0.12
Rv3236c 3612665 p.Val151Ala missense_variant 0.49
ddn 3987057 p.Arg72Gly missense_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 0.38
clpC1 4040719 c.-15A>G upstream_gene_variant 0.42
embC 4240671 p.Thr270Ile missense_variant 0.37
embC 4241042 p.Asn394Asp missense_variant 0.46
embC 4242075 p.Arg738Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243854 p.Leu208Phe missense_variant 0.51
embA 4245969 p.Pro913Ser missense_variant 0.38
embB 4246430 c.-84C>T upstream_gene_variant 0.39
embB 4247646 p.Glu378Ala missense_variant 0.42
aftB 4267925 c.912G>A synonymous_variant 0.53
aftB 4267960 p.Val293Met missense_variant 0.38
ubiA 4269387 p.Glu149Asp missense_variant 0.29
aftB 4269606 c.-770T>C upstream_gene_variant 0.41
ethA 4326148 c.1326G>T synonymous_variant 0.34
ethA 4326439 p.Asn345Lys missense_variant 0.4
whiB6 4338203 p.Arg107Cys missense_variant 0.38
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.37
gid 4407588 c.615A>G synonymous_variant 0.48
gid 4407848 p.Ala119Thr missense_variant 0.48
gid 4407873 c.330G>T synonymous_variant 0.51