TB-Profiler result

Run: ERR4817114
Summary

Run ID: ERR4817114

Sample name:

Date: 01-04-2023 14:48:39

Number of reads: 485782

Percentage reads mapped: 98.64

Strain:

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
lineage1.2.1.2 Indo-Oceanic NA RD239 0.98
lineage1.2.1.2.1 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
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 5154 c.-85delG upstream_gene_variant 0.17
gyrB 5727 p.Pro163Gln missense_variant 0.29
gyrB 6112 p.Met291Ile missense_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 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490694 c.-89G>T upstream_gene_variant 0.2
fgd1 490986 c.204G>A synonymous_variant 0.29
fgd1 491528 p.Trp249* stop_gained 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 576536 p.Gln397Lys missense_variant 0.25
ccsA 620086 p.Asp66Asn missense_variant 0.13
rpoB 759848 p.Ser14Arg missense_variant 0.25
rpoB 762229 p.Leu808Pro missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764809 c.1440C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776693 c.1788C>G synonymous_variant 0.18
mmpL5 777713 c.768T>A synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800837 p.Lys10Arg missense_variant 0.33
rplC 801016 p.Tyr70His missense_variant 0.17
fbiC 1302821 c.-110G>A upstream_gene_variant 1.0
fbiC 1303364 p.Phe145Tyr missense_variant 0.33
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406579 p.His254Gln missense_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918189 p.Arg84Gly missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156418 c.-307G>T upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169302 p.Met437Ile missense_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518300 c.186T>G synonymous_variant 0.25
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3065276 c.915delC frameshift_variant 0.25
Rv2752c 3065891 p.Pro101Ala missense_variant 0.2
thyX 3067453 c.491_492delGC frameshift_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087661 c.844_845dupAC frameshift_variant 0.4
fbiD 3339417 c.300A>G synonymous_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
fprA 3475189 p.Cys395Arg missense_variant 0.25
whiB7 3568488 c.191delG frameshift_variant 1.0
whiB7 3568866 c.-187C>T upstream_gene_variant 0.13
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
clpC1 4039682 c.1023C>G synonymous_variant 0.5
clpC1 4039694 c.1011G>C synonymous_variant 0.4
clpC1 4039724 c.981A>G synonymous_variant 0.2
clpC1 4039733 c.972G>A synonymous_variant 0.2
clpC1 4039739 c.966C>G synonymous_variant 0.2
clpC1 4039742 c.963C>T synonymous_variant 0.2
clpC1 4039748 c.957G>C synonymous_variant 0.22
clpC1 4039751 c.954A>G synonymous_variant 0.22
clpC1 4040026 p.Glu227Lys missense_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241125 c.1263G>C synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embB 4245794 c.-720G>A upstream_gene_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246926 p.Glu138Gly missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268247 p.Leu197Pro missense_variant 0.22
aftB 4268249 c.588G>T synonymous_variant 0.22
aftB 4268359 p.Gln160Glu missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4328209 c.-736C>A upstream_gene_variant 0.22
whiB6 4338361 p.Arg54Gln 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 4407873 c.330G>T synonymous_variant 1.0