TB-Profiler result

Run: ERR2514109
Summary

Run ID: ERR2514109

Sample name:

Date: 31-03-2023 20:07:24

Number of reads: 444540

Percentage reads mapped: 99.53

Strain: lineage2.2.1

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
katG 2154172 c.1939delA frameshift_variant 0.12 isoniazid
embB 4247622 p.Leu370Arg missense_variant 1.0 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 6043 c.804G>A synonymous_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760076 c.270C>T synonymous_variant 0.15
rpoB 760301 c.495C>A synonymous_variant 0.11
rpoB 761299 p.Ala498Glu missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764242 c.873C>T synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776158 p.Asp775His missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302984 c.54G>T synonymous_variant 0.13
fbiC 1305302 p.Leu791Pro missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473086 n.1244delA non_coding_transcript_exon_variant 0.29
rrl 1476061 n.2404T>C non_coding_transcript_exon_variant 0.67
fabG1 1674151 p.Pro238Thr missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102816 p.Leu76Pro missense_variant 0.12
ndh 2103225 c.-183A>C upstream_gene_variant 0.4
katG 2154088 p.Asp675Gly missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168524 p.Gly697Ser missense_variant 0.17
Rv1979c 2222300 p.Val289Met missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726495 p.Asn101Lys missense_variant 0.22
folC 2746526 p.Gly358Val missense_variant 0.14
pepQ 2860208 p.Leu71Val missense_variant 0.18
Rv2752c 3064589 p.Arg535Ser missense_variant 0.25
thyA 3074554 c.-83G>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339569 p.Leu151Pro missense_variant 0.29
Rv3083 3449458 p.Asp319Asn missense_variant 0.15
fprA 3473906 c.-101A>G upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640386 c.-157A>G upstream_gene_variant 0.22
rpoA 3878425 p.Pro28Leu missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245169 p.Val646Ala missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326491 p.Asn328Ile missense_variant 0.1
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0