TB-Profiler result

Run: ERR4818415
Summary

Run ID: ERR4818415

Sample name:

Date: 01-04-2023 15:32:35

Number of reads: 543818

Percentage reads mapped: 99.13

Strain: lineage1.2.2.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8552 c.1251C>T synonymous_variant 0.18
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9685 p.Gly795Val missense_variant 0.14
fgd1 491548 p.Ala256Ser missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575464 c.117G>A synonymous_variant 0.11
mshA 576742 c.1395G>A synonymous_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763552 c.183C>T synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764483 c.1114C>A synonymous_variant 0.4
rpoC 766036 c.2667C>T synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777663 p.Ala273Val missense_variant 0.18
mmpS5 779625 c.-720G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303468 p.Arg180Cys missense_variant 0.12
fbiC 1303676 p.Gly249Asp missense_variant 0.15
fbiC 1303723 p.Glu265Lys missense_variant 0.14
embR 1416887 p.Arg154His missense_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473559 n.-99G>A upstream_gene_variant 0.67
inhA 1673419 c.-783G>A upstream_gene_variant 1.0
fabG1 1673621 p.Asp61Gly missense_variant 0.2
rpsA 1833554 p.Thr5Ala missense_variant 0.11
rpsA 1833568 c.27G>C synonymous_variant 0.12
rpsA 1833589 c.48A>T synonymous_variant 0.12
rpsA 1833595 c.54T>C synonymous_variant 0.12
rpsA 1834850 p.Ala437Thr missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918151 p.Val71Ala missense_variant 1.0
ndh 2102240 p.Arg268His missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168104 p.Pro837Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222610 c.555C>T synonymous_variant 0.17
Rv1979c 2222868 c.297C>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.92
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714412 c.921G>A synonymous_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859408 c.1011C>T synonymous_variant 0.14
Rv2752c 3065769 c.423C>T synonymous_variant 0.12
Rv2752c 3066151 p.Gly14Asp missense_variant 0.15
Rv2752c 3066153 c.39C>T synonymous_variant 0.14
thyA 3074338 p.Leu45Pro missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448376 c.-128G>T upstream_gene_variant 0.2
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
fbiB 3640908 c.-627C>T upstream_gene_variant 0.18
rpoA 3877635 c.873G>A synonymous_variant 0.17
clpC1 4039969 p.Gln246Lys missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0
clpC1 4040874 c.-171delT upstream_gene_variant 0.33
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 4245670 p.Ala813Gly missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246979 p.Gly156Cys missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248045 p.Lys511Arg missense_variant 0.12
embB 4248779 p.Glu756Lys missense_variant 0.13
aftB 4267559 c.1278C>T synonymous_variant 1.0
aftB 4267960 p.Val293Met missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269440 p.Leu132Phe missense_variant 0.12
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_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 4407848 p.Ala119Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408273 c.-71C>T upstream_gene_variant 0.18