TB-Profiler result

Run: SRR25827617
Summary

Run ID: SRR25827617

Sample name:

Date: 02-02-2024 11:38:41

Number of reads: 5548222

Percentage reads mapped: 99.42

Strain: lineage3;lineage2.2.1;lineage1.2.2.2

Drug-resistance: 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 (0.68)
Isoniazid R katG p.Ser315Thr (0.93)
Ethambutol R embB p.Met306Val (0.61)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.55), rrs n.517C>T (0.37)
Fluoroquinolones R gyrA p.Asp94Gly (0.58)
Moxifloxacin R gyrA p.Asp94Gly (0.58)
Ofloxacin R gyrA p.Asp94Gly (0.58)
Levofloxacin R gyrA p.Asp94Gly (0.58)
Ciprofloxacin R gyrA p.Asp94Gly (0.58)
Aminoglycosides
Amikacin
Capreomycin R tlyA c.589dupG (0.33)
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.40)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.28
lineage2 East-Asian Beijing RD105 0.46
lineage1 Indo-Oceanic EAI RD239 0.2
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.48
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.24
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.47
lineage1.2.2.2 Indo-Oceanic NA RD239 0.15
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 0.58 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.55 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.4 linezolid
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.37 streptomycin
tlyA 1918524 c.589dupG frameshift_variant 0.33 capreomycin
katG 2155168 p.Ser315Thr missense_variant 0.93 isoniazid
embB 4247429 p.Met306Val missense_variant 0.61 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
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 0.3
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490977 c.195C>G synonymous_variant 0.45
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.36
ccsA 620553 c.663T>C synonymous_variant 0.32
ccsA 620625 p.Ile245Met missense_variant 0.47
rpoB 759746 c.-61C>T upstream_gene_variant 0.24
rpoC 763031 c.-339T>C upstream_gene_variant 0.91
rpoC 763884 p.Ala172Val missense_variant 0.31
rpoC 763886 c.517C>A synonymous_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.54
mmpR5 779127 c.139dupG frameshift_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.33
embR 1416814 c.534G>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.62
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.22
ndh 2102359 c.683delT frameshift_variant 0.34
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.96
PPE35 2168742 p.Gly624Asp missense_variant 0.21
Rv1979c 2222308 p.Asp286Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288683 c.559T>G stop_lost&splice_region_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 0.26
ahpC 2726051 c.-142G>A upstream_gene_variant 0.29
ahpC 2726105 c.-88G>A upstream_gene_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.26
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54
clpC1 4040517 p.Val63Ala missense_variant 0.38
panD 4044023 c.259C>T synonymous_variant 0.26
embC 4240671 p.Thr270Ile missense_variant 0.5
embC 4242075 p.Arg738Gln missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.33
embA 4245969 p.Pro913Ser missense_variant 0.26
embB 4247646 p.Glu378Ala missense_variant 0.4
embB 4249757 p.Thr1082Ala missense_variant 0.55
aftB 4267647 p.Asp397Gly missense_variant 0.33
ubiA 4269387 p.Glu149Asp missense_variant 0.2
aftB 4269606 c.-770T>C upstream_gene_variant 0.26
ethA 4326148 c.1326G>T synonymous_variant 0.45
whiB6 4338203 p.Arg107Cys missense_variant 0.3
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 0.88
gid 4407848 p.Ala119Thr missense_variant 0.39
gid 4407873 c.330G>T synonymous_variant 0.39
gid 4407927 p.Glu92Asp missense_variant 0.44