TB-Profiler result

Run: SRR25827550

Summary

Run ID: SRR25827550

Sample name:

Date: 15-02-2024 05:24:41

Number of reads: 8791575

Percentage reads mapped: 99.2

Strain: lineage3.1;lineage2.2.1;lineage1.1.2

Drug-resistance: Pre-XDR-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.Asp435Tyr (0.24), rpoB p.Ser450Leu (0.42)
Isoniazid R katG p.Ser315Thr (0.66)
Ethambutol R embA c.-16C>T (0.38), embB p.Gln497Lys (0.27)
Pyrazinamide R pncA p.Ile5Ser (0.42)
Streptomycin R rpsL p.Lys43Arg (0.34)
Fluoroquinolones R gyrA p.Ser91Pro (0.23), gyrA p.Asp94Gly (0.42)
Moxifloxacin R gyrA p.Ser91Pro (0.23), gyrA p.Asp94Gly (0.42)
Ofloxacin R gyrA p.Ser91Pro (0.23), gyrA p.Asp94Gly (0.42)
Levofloxacin R gyrA p.Ser91Pro (0.23), gyrA p.Asp94Gly (0.42)
Ciprofloxacin R gyrA p.Ser91Pro (0.23), gyrA p.Asp94Gly (0.42)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-10G>A (0.42)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.39)
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 0.27
lineage2 East-Asian Beijing RD105 0.41
lineage1 Indo-Oceanic EAI RD239 0.31
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.34
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.39
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.23
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.32
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.4
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
gyrA 7572 p.Ser91Pro missense_variant 0.23 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.42 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 0.24 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.42 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.34 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.66 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.42 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.42 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.39 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 0.38 ethambutol
embB 4248002 p.Gln497Lys missense_variant 0.27 ethambutol
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 0.3
gyrB 6124 c.885C>T synonymous_variant 0.32
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.35
gyrA 9143 c.1842T>C synonymous_variant 0.35
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.36
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.41
ccsA 620625 p.Ile245Met missense_variant 0.41
rpoB 759746 c.-61C>T upstream_gene_variant 0.28
rpoB 760490 c.684C>T synonymous_variant 0.29
rpoC 762434 c.-936T>G upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.34
rpoC 763886 c.517C>A synonymous_variant 0.33
rpoC 764703 p.Lys445Arg missense_variant 0.42
rpoC 765171 p.Pro601Leu missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.36
mmpL5 776395 p.Phe696Leu missense_variant 0.33
mmpR5 779460 p.Tyr157* stop_gained 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 0.44
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.42
embR 1417019 p.Cys110Tyr missense_variant 0.35
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476685 n.3028A>T non_coding_transcript_exon_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156123 c.-12G>T upstream_gene_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2167983 p.Gly877Asp missense_variant 0.36
PPE35 2170173 p.Asp147Ala missense_variant 0.38
Rv1979c 2222308 p.Asp286Gly missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.3
pncA 2289365 c.-125delC upstream_gene_variant 0.25
kasA 2518132 c.18C>T synonymous_variant 0.39
ahpC 2726051 c.-142G>A upstream_gene_variant 0.29
ahpC 2726105 c.-88G>A upstream_gene_variant 0.3
ribD 2987538 p.Val234Met missense_variant 0.25
Rv2752c 3064632 c.1560C>T synonymous_variant 0.34
thyX 3067949 c.-4C>T upstream_gene_variant 0.47
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.32
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.33
fprA 3475159 p.Asn385Asp missense_variant 0.34
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4
clpC1 4040178 p.Arg176His missense_variant 0.24
clpC1 4040517 p.Val63Ala missense_variant 0.4
embC 4240671 p.Thr270Ile missense_variant 0.3
embC 4241022 p.Ala387Val missense_variant 0.4
embC 4241042 p.Asn394Asp missense_variant 0.35
embC 4242075 p.Arg738Gln missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>T upstream_gene_variant 0.26
embA 4243460 c.228C>T synonymous_variant 0.39
embA 4243848 p.Val206Met missense_variant 0.33
embA 4245218 c.1986C>T synonymous_variant 0.34
embA 4245969 p.Pro913Ser missense_variant 0.3
embB 4247028 p.Leu172Arg missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 0.33
embB 4247847 p.Gln445Arg missense_variant 0.42
aftB 4267647 p.Asp397Gly missense_variant 0.45
ubiA 4269031 p.Gly268Asp missense_variant 0.38
ubiA 4269387 p.Glu149Asp missense_variant 0.35
aftB 4269606 c.-770T>C upstream_gene_variant 0.31
ethA 4327060 p.Ser138Arg missense_variant 0.41
whiB6 4338354 p.Cys56* stop_gained 0.29
whiB6 4338397 p.Thr42Met missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 0.97
whiB6 4338603 c.-82C>T upstream_gene_variant 0.31
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407618 p.Tyr195Gln missense_variant 0.23
gid 4407873 c.330G>T synonymous_variant 0.37
gid 4407927 p.Glu92Asp missense_variant 0.37