TB-Profiler result

Run: SRR25827862
Summary

Run ID: SRR25827862

Sample name:

Date: 02-02-2024 22:56:50

Number of reads: 3086847

Percentage reads mapped: 49.87

Strain: lineage2.2.1.1;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.Ser450Leu (0.70)
Isoniazid R katG p.Ser315Thr (0.95)
Ethambutol R embB p.Met306Val (0.59)
Pyrazinamide R pncA p.Val139Ala (0.66)
Streptomycin R rpsL p.Lys43Arg (0.68)
Fluoroquinolones R gyrA p.Asp94Gly (0.66)
Moxifloxacin R gyrA p.Asp94Gly (0.66)
Ofloxacin R gyrA p.Asp94Gly (0.66)
Levofloxacin R gyrA p.Asp94Gly (0.66)
Ciprofloxacin R gyrA p.Asp94Gly (0.66)
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
lineage2 East-Asian Beijing RD105 0.62
lineage1 Indo-Oceanic EAI RD239 0.36
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.41
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.66
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.39
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.61
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.62
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 7582 p.Asp94Gly missense_variant 0.66 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.7 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.68 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
pncA 2288826 p.Val139Ala missense_variant 0.66 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.59 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 0.38
gyrB 6124 c.885C>T synonymous_variant 0.37
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.42
gyrA 9047 c.1746C>T synonymous_variant 0.4
gyrA 9143 c.1842T>C synonymous_variant 0.47
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 0.3
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.58
mshA 576000 p.Asp218Ala missense_variant 0.32
mshA 576468 p.Val374Gly missense_variant 0.17
mshA 576651 p.Asp435Ala missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 0.58
rpoB 760490 c.684C>T synonymous_variant 0.47
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.29
rpoC 763886 c.517C>A synonymous_variant 0.3
rpoC 764363 p.Gly332Ser missense_variant 0.85
rpoC 765171 p.Pro601Leu missense_variant 0.37
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.67
mmpL5 776395 p.Phe696Leu missense_variant 0.36
mmpS5 779615 c.-710C>G upstream_gene_variant 0.66
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.63
embR 1417019 p.Cys110Tyr missense_variant 0.32
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.53
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 0.39
Rv1979c 2222308 p.Asp286Gly missense_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.38
eis 2714846 p.Val163Ile missense_variant 0.65
ahpC 2726051 c.-142G>A upstream_gene_variant 0.32
Rv2752c 3064632 c.1560C>T synonymous_variant 0.45
Rv2752c 3065305 p.Ala296Val missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.39
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.45
fprA 3475159 p.Asn385Asp missense_variant 0.39
Rv3236c 3612813 p.Thr102Ala missense_variant 0.73
clpC1 4040517 p.Val63Ala missense_variant 0.39
embC 4240671 p.Thr270Ile missense_variant 0.29
embC 4241042 p.Asn394Asp missense_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243340 c.108G>A synonymous_variant 0.32
embA 4243460 c.228C>T synonymous_variant 0.61
embA 4243848 p.Val206Met missense_variant 0.46
embA 4245969 p.Pro913Ser missense_variant 0.42
embB 4247646 p.Glu378Ala missense_variant 0.4
embB 4247880 p.Val456Ala missense_variant 0.54
embB 4248115 c.1602C>T synonymous_variant 0.51
aftB 4267647 p.Asp397Gly missense_variant 0.63
ubiA 4269387 p.Glu149Asp missense_variant 0.4
aftB 4269606 c.-770T>C upstream_gene_variant 0.37
whiB6 4338410 p.Pro38Ala missense_variant 0.62
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.4
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.38
gid 4407927 p.Glu92Asp missense_variant 0.68
gid 4408125 p.Leu26Phe missense_variant 0.32