TB-Profiler result

Run: ERR4797100
Summary

Run ID: ERR4797100

Sample name:

Date: 01-04-2023 07:21:34

Number of reads: 5036776

Percentage reads mapped: 99.59

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
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.8
lineage1 Indo-Oceanic EAI RD239 0.18
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.12
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.18
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 761110 p.Asp435Val missense_variant 0.73 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.18 streptomycin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.75 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.84 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289207 p.Asp12Ala missense_variant 0.82 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 0.81 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 0.31
gyrA 9143 c.1842T>C synonymous_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9360 p.Asp687Asn missense_variant 0.14
fgd1 490756 c.-27T>G upstream_gene_variant 0.19
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.82
rpoB 760490 c.684C>T synonymous_variant 0.27
rpoC 762434 c.-936T>G upstream_gene_variant 0.82
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.21
rpoC 763886 c.517C>A synonymous_variant 0.19
rpoC 765857 p.Glu830Gln missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 0.16
mmpL5 777626 c.855C>T synonymous_variant 0.81
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.18
atpE 1460904 c.-141C>T upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471793 n.-53G>T upstream_gene_variant 0.26
rrl 1473626 n.-32C>G upstream_gene_variant 0.25
rrl 1474500 n.843T>A non_coding_transcript_exon_variant 0.4
rrl 1474658 n.1001A>T non_coding_transcript_exon_variant 0.13
rrl 1476261 n.2604A>G non_coding_transcript_exon_variant 0.11
fabG1 1673553 p.Asp38Glu missense_variant 0.36
fabG1 1673558 p.His40Pro missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103184 c.-142G>T upstream_gene_variant 0.8
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156187 c.-76G>A upstream_gene_variant 0.65
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167979 c.2634A>G synonymous_variant 0.12
PPE35 2167983 p.Gly877Asp missense_variant 0.16
PPE35 2170785 c.-173T>C upstream_gene_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.96
pncA 2289365 c.-125delC upstream_gene_variant 0.68
kasA 2518132 c.18C>T synonymous_variant 0.19
kasA 2519071 p.Asp319Glu missense_variant 0.16
eis 2714545 p.Glu263Val missense_variant 0.48
eis 2715016 p.Arg106His missense_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 0.28
ahpC 2726105 c.-88G>A upstream_gene_variant 0.7
pepQ 2860159 p.Ala87Gly missense_variant 0.25
Rv2752c 3064632 c.1560C>T synonymous_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
Rv3083 3448440 c.-64A>C upstream_gene_variant 0.83
Rv3083 3448714 p.Asp71His missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474213 p.Lys69Asn missense_variant 0.15
fprA 3474597 c.591C>A synonymous_variant 0.21
fprA 3475159 p.Asn385Asp missense_variant 0.25
alr 3841473 c.-53G>A upstream_gene_variant 0.89
rpoA 3878575 c.-68C>A upstream_gene_variant 0.75
clpC1 4040517 p.Val63Ala missense_variant 0.19
embC 4240409 p.Pro183Ala missense_variant 0.14
embC 4241042 p.Asn394Asp missense_variant 0.16
embC 4242075 p.Arg738Gln missense_variant 0.84
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.21
embA 4245969 p.Pro913Ser missense_variant 0.3
embB 4247646 p.Glu378Ala missense_variant 0.26
aftB 4267466 p.Tyr457* stop_gained 0.13
aftB 4268540 p.Met99Ile missense_variant 0.23
aftB 4268619 p.Val73Gly missense_variant 0.26
aftB 4268868 c.-32G>T upstream_gene_variant 0.11
ubiA 4269387 p.Glu149Asp missense_variant 0.23
aftB 4269606 c.-770T>C upstream_gene_variant 0.1
whiB6 4338200 p.Asp108His missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.18
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407733 p.Gly157Glu missense_variant 0.8
gid 4407873 c.330G>T synonymous_variant 0.12