TB-Profiler result

Run: ERR4821757
Summary

Run ID: ERR4821757

Sample name:

Date: 01-04-2023 17:26:09

Number of reads: 1395906

Percentage reads mapped: 99.45

Strain: lineage1.1.2

Drug-resistance: Sensitive

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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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 1.0
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
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 5807 p.Val190Ile missense_variant 0.15
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrB 6679 c.1441_1442delCT frameshift_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7372 p.Met24Thr missense_variant 0.1
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8849 c.1548C>A synonymous_variant 0.22
gyrA 8884 p.Arg528His missense_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576710 c.1367delG frameshift_variant 0.11
rpoB 759803 c.-4C>G upstream_gene_variant 0.12
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 762298 p.Leu831Pro missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764828 p.Leu487Val missense_variant 0.1
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765233 p.Ala622Thr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.96
mmpL5 776395 p.Phe696Leu missense_variant 0.95
mmpR5 778019 c.-971C>T upstream_gene_variant 0.11
mmpR5 778043 c.-947G>A upstream_gene_variant 0.14
mmpS5 778593 p.Ala105Thr missense_variant 0.15
mmpR5 779247 c.262delG frameshift_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781806 p.Arg83Cys missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460931 c.-113delT upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471698 n.-148A>C upstream_gene_variant 0.15
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 1.0
rpsA 1834492 c.951C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155796 p.Ala106Thr missense_variant 0.12
katG 2156109 c.3G>T synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168717 c.1896G>A synonymous_variant 0.18
PPE35 2168939 p.Leu558Phe missense_variant 0.12
PPE35 2170165 p.Ala150Thr missense_variant 0.14
Rv1979c 2222277 c.888A>G synonymous_variant 0.17
Rv1979c 2222308 p.Asp286Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715016 p.Arg106His missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3613114 c.3G>T synonymous_variant 0.18
fbiB 3642351 p.Gly273Cys missense_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040588 c.117T>C synonymous_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247905 c.1392G>C synonymous_variant 1.0
ubiA 4269145 p.Val230Ala missense_variant 0.11
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407624 c.579G>A synonymous_variant 0.12
gid 4407873 c.330G>T synonymous_variant 1.0