TB-Profiler result

Run: ERR2446091
Summary

Run ID: ERR2446091

Sample name:

Date: 15-08-2022 11:02:47

Number of reads: 357173

Percentage reads mapped: 99.98

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 0.98
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6113 p.Gln292Lys missense_variant 0.14
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 6454 c.-848C>A upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9096 p.Leu599Met missense_variant 0.2
gyrA 9592 p.Gly764Val missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 762945 p.Thr1047Ser missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765930 p.His854Leu missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775644 p.Arg946Leu missense_variant 0.14
mmpL5 775697 c.2784G>A synonymous_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472595 n.750A>G non_coding_transcript_exon_variant 0.12
rrs 1473055 n.1210C>A non_coding_transcript_exon_variant 0.12
rrl 1475058 n.1401C>T non_coding_transcript_exon_variant 0.18
rrl 1476389 n.2732G>T non_coding_transcript_exon_variant 0.18
rpsA 1834493 p.Glu318* stop_gained 0.23
ndh 2102587 p.Leu152Phe missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169201 p.Ser471* stop_gained 0.2
PPE35 2170628 c.-16C>A upstream_gene_variant 0.2
PPE35 2170669 c.-57G>T upstream_gene_variant 0.2
Rv1979c 2221746 c.1419G>T synonymous_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289137 c.105G>A synonymous_variant 1.0
ribD 2986910 c.72C>A synonymous_variant 0.15
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449229 c.726T>C synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.89
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475039 p.Gly345Cys missense_variant 0.18
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568507 p.Gln58Arg missense_variant 1.0
Rv3236c 3613297 c.-181C>T upstream_gene_variant 1.0
alr 3840431 c.990C>A synonymous_variant 0.2
clpC1 4040330 c.375C>A synonymous_variant 0.12
embA 4243933 p.Arg234Leu missense_variant 0.2
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248732 p.Val740Ala missense_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ethA 4327467 p.Glu3* stop_gained 0.2
ethA 4328157 c.-684C>A upstream_gene_variant 0.15
whiB6 4338441 p.Tyr27* stop_gained 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 4407873 c.330G>T synonymous_variant 1.0