TB-Profiler result

Run: ERR4830355
Summary

Run ID: ERR4830355

Sample name:

Date: 01-04-2023 20:07:29

Number of reads: 3701860

Percentage reads mapped: 98.8

Strain: lineage2.2.1;lineage1.1.1.1

Drug-resistance: HR-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
lineage2 East-Asian Beijing RD105 0.19
lineage1 Indo-Oceanic EAI RD239 0.74
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.77
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.24
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.24
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.77
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.8
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.72 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.79 isoniazid, ethionamide
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 0.86
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.82
gyrA 9143 c.1842T>C synonymous_variant 0.83
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490972 p.Arg64Ser missense_variant 0.77
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.87
rpoC 763886 c.517C>A synonymous_variant 0.87
rpoC 764696 c.1327C>T synonymous_variant 0.76
rpoC 765171 p.Pro601Leu missense_variant 0.72
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.16
mmpL5 777581 p.Tyr300* stop_gained 0.79
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.2
Rv1258c 1407255 p.Ala29Val missense_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 0.78
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.76
rpsA 1834177 c.636A>C synonymous_variant 0.28
rpsA 1834319 p.Val260Ile missense_variant 0.8
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156389 c.-278G>C upstream_gene_variant 0.86
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.79
Rv1979c 2222308 p.Asp286Gly missense_variant 0.82
Rv1979c 2222918 c.245_246delCA frameshift_variant 0.74
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.78
kasA 2519258 p.Leu382Ile missense_variant 0.25
ahpC 2726051 c.-142G>A upstream_gene_variant 0.78
Rv2752c 3064632 c.1560C>T synonymous_variant 0.77
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.85
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.81
fprA 3475159 p.Asn385Asp missense_variant 0.84
Rv3236c 3612567 p.Gly184Cys missense_variant 0.66
Rv3236c 3612813 p.Thr102Ala missense_variant 0.19
alr 3841329 p.Thr31Ile missense_variant 0.81
rpoA 3878630 c.-124delC upstream_gene_variant 0.79
clpC1 4040517 p.Val63Ala missense_variant 0.74
embC 4240671 p.Thr270Ile missense_variant 0.74
embC 4241042 p.Asn394Asp missense_variant 0.64
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.32
embA 4243848 p.Val206Met missense_variant 0.68
embA 4244096 c.864C>T synonymous_variant 0.79
embA 4245712 p.Ala827Gly missense_variant 0.31
embA 4245969 p.Pro913Ser missense_variant 0.69
embB 4247646 p.Glu378Ala missense_variant 0.45
aftB 4267143 p.Ala565Gly missense_variant 0.16
aftB 4267647 p.Asp397Gly missense_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 0.76
aftB 4269606 c.-770T>C upstream_gene_variant 0.76
whiB6 4338242 p.Gln94Glu missense_variant 0.81
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.78
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.74
gid 4407927 p.Glu92Asp missense_variant 0.27