TB-Profiler result

Run: ERR4799036

Summary

Run ID: ERR4799036

Sample name:

Date: 01-04-2023 08:49:28

Number of reads: 3285832

Percentage reads mapped: 99.57

Strain: lineage4;lineage3.1.2.1;lineage2.2.1;lineage1.2.2.2

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
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.34
lineage2 East-Asian Beijing RD105 0.24
lineage4 Euro-American LAM;T;S;X;H None 0.12
lineage1 Indo-Oceanic EAI RD239 0.31
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.25
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.17
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.31
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.2
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.23
lineage1.2.2.2 Indo-Oceanic NA RD239 0.31
lineage3.1.2.1 East-African-Indian CAS2 RD750 0.14
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 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.37 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.23 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.13 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.36 isoniazid
embB 4247429 p.Met306Val missense_variant 0.16 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 5075 c.-165C>T upstream_gene_variant 0.32
gyrB 6112 p.Met291Ile missense_variant 0.24
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.96
gyrA 8452 p.Ala384Val missense_variant 0.33
gyrA 9143 c.1842T>C synonymous_variant 0.49
gyrA 9163 p.Pro621Leu missense_variant 0.45
gyrA 9304 p.Gly668Asp missense_variant 0.94
fgd1 491290 p.Val170Met missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 0.86
mshA 575907 p.Ala187Val missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 0.26
rpoB 759746 c.-61C>T upstream_gene_variant 0.32
rpoC 762434 c.-936T>G upstream_gene_variant 0.25
rpoC 762800 c.-570C>T upstream_gene_variant 0.28
rpoC 763031 c.-339T>C upstream_gene_variant 0.84
rpoC 763884 p.Ala172Val missense_variant 0.34
rpoC 763886 c.517C>A synonymous_variant 0.34
rpoC 764840 p.Ile491Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 776182 p.Asp767Asn missense_variant 0.26
mmpS5 779615 c.-710C>G upstream_gene_variant 0.23
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.28
embR 1417019 p.Cys110Tyr missense_variant 0.33
embR 1417167 p.Glu61Lys missense_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 0.87
PPE35 2168604 p.Pro670Leu missense_variant 0.21
PPE35 2168742 p.Gly624Asp missense_variant 0.28
Rv1979c 2222308 p.Asp286Gly missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.38
pncA 2289365 c.-125delC upstream_gene_variant 0.43
kasA 2518132 c.18C>T synonymous_variant 0.36
ahpC 2726051 c.-142G>A upstream_gene_variant 0.23
ahpC 2726105 c.-88G>A upstream_gene_variant 0.25
Rv2752c 3064889 p.Lys435Glu missense_variant 0.26
thyA 3073868 p.Thr202Ala missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 0.97
Rv3083 3448714 p.Asp71His missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
fprA 3474597 c.591C>A synonymous_variant 0.35
fprA 3475159 p.Asn385Asp missense_variant 0.34
Rv3236c 3612813 p.Thr102Ala missense_variant 0.2
alr 3841444 c.-24G>A upstream_gene_variant 0.24
alr 3841546 c.-126C>A upstream_gene_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.26
embC 4240671 p.Thr270Ile missense_variant 0.34
embC 4241042 p.Asn394Asp missense_variant 0.26
embC 4242075 p.Arg738Gln missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242802 c.-431G>A upstream_gene_variant 0.29
embA 4243460 c.228C>T synonymous_variant 0.25
embA 4245969 p.Pro913Ser missense_variant 0.3
embB 4247646 p.Glu378Ala missense_variant 0.24
aftB 4267647 p.Asp397Gly missense_variant 0.21
ubiA 4269387 p.Glu149Asp missense_variant 0.24
aftB 4269537 c.-701G>A upstream_gene_variant 0.24
aftB 4269606 c.-770T>C upstream_gene_variant 0.33
ethA 4326439 p.Asn345Lys missense_variant 0.35
ethA 4328212 c.-740delC upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.33
whiB6 4338635 c.-114A>C upstream_gene_variant 0.4
gid 4407588 c.615A>G synonymous_variant 0.93
gid 4407620 p.Tyr195His missense_variant 0.12
gid 4407873 c.330G>T synonymous_variant 0.3
gid 4407927 p.Glu92Asp missense_variant 0.25
gid 4408020 c.183C>T synonymous_variant 0.33