TB-Profiler result

Run: SRR25827857
Summary

Run ID: SRR25827857

Sample name:

Date: 02-02-2024 22:36:37

Number of reads: 10238543

Percentage reads mapped: 98.86

Strain: lineage3;lineage1.1.2

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 (0.29)
Isoniazid R katG p.Ser315Thr (0.27)
Ethambutol R embB p.Met306Ile (0.23)
Pyrazinamide
Streptomycin R gid c.351delG (0.21)
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 0.78
lineage1 Indo-Oceanic EAI RD239 0.2
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.19
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.21
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 0.29 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.27 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.23 ethambutol
gid 4407851 c.351delG frameshift_variant 0.21 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 6112 p.Met291Ile missense_variant 0.2
gyrB 6124 c.885C>T synonymous_variant 0.2
gyrB 6963 p.Arg575His missense_variant 0.43
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 0.19
gyrA 9143 c.1842T>C synonymous_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 0.83
rpoB 760490 c.684C>T synonymous_variant 0.22
rpoB 761074 p.Glu423Gly missense_variant 0.3
rpoC 762434 c.-936T>G upstream_gene_variant 0.8
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.19
rpoC 763886 c.517C>A synonymous_variant 0.2
rpoC 765171 p.Pro601Leu missense_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776181 p.Asp767Ala missense_variant 0.39
mmpL5 776395 p.Phe696Leu missense_variant 0.24
mmpL5 777444 p.Val346Ala missense_variant 0.47
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.23
Rv1979c 2222308 p.Asp286Gly missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.83
kasA 2518132 c.18C>T synonymous_variant 0.27
ahpC 2726051 c.-142G>A upstream_gene_variant 0.19
ahpC 2726105 c.-88G>A upstream_gene_variant 0.8
Rv2752c 3064632 c.1560C>T synonymous_variant 0.23
Rv2752c 3065305 p.Ala296Val missense_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.17
Rv3083 3449722 p.Cys407Gly missense_variant 0.44
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.21
fprA 3475159 p.Asn385Asp missense_variant 0.2
fbiA 3640618 p.Gly26Ser missense_variant 0.38
fbiA 3640766 p.Pro75Leu missense_variant 0.27
fbiB 3642877 p.Lys448Arg missense_variant 0.21
alr 3841046 c.375G>A synonymous_variant 0.2
alr 3841590 c.-170G>A upstream_gene_variant 0.47
ddn 3987057 p.Arg72Trp missense_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 0.19
embC 4241042 p.Asn394Asp missense_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 0.79
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.18
embA 4243901 c.669G>A synonymous_variant 0.27
embA 4245969 p.Pro913Ser missense_variant 0.21
embB 4247028 p.Leu172Arg missense_variant 0.16
embB 4247646 p.Glu378Ala missense_variant 0.22
aftB 4268719 p.Asn40Asp missense_variant 0.4
ubiA 4269387 p.Glu149Asp missense_variant 0.15
aftB 4269606 c.-770T>C upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.23
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.22
gid 4408084 p.Glu40Gly missense_variant 0.29
gid 4408251 c.-49T>C upstream_gene_variant 0.16