TB-Profiler result

Run: ERR3077959
Summary

Run ID: ERR3077959

Sample name:

Date: 01-04-2023 00:12:38

Number of reads: 632460

Percentage reads mapped: 99.46

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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
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 490751 c.-32T>G upstream_gene_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575294 c.-54C>T upstream_gene_variant 0.29
mshA 576354 p.Leu336Pro missense_variant 0.11
mshA 576751 p.Lys468Asn missense_variant 0.62
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761043 p.Asn413Asp missense_variant 0.13
rpoC 762434 c.-936T>G upstream_gene_variant 0.94
rpoC 762824 c.-546C>T upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777471 p.Val337Ala missense_variant 0.13
mmpL5 778804 c.-324C>T upstream_gene_variant 0.12
mmpS5 779675 c.-770G>A upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406671 p.Val224Ile missense_variant 0.15
Rv1258c 1407387 c.-47T>A upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103199 c.-157G>A upstream_gene_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168105 c.2508C>G synonymous_variant 0.11
PPE35 2170461 p.Gly51Glu missense_variant 0.9
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2715327 c.6T>C synonymous_variant 0.11
eis 2715505 c.-173A>G upstream_gene_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860050 c.369G>A synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087012 c.196delG frameshift_variant 0.12
Rv3083 3448596 c.93A>G synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568737 c.-58C>T upstream_gene_variant 1.0
Rv3236c 3612835 c.282T>G synonymous_variant 0.24
alr 3840247 p.Thr392Ala missense_variant 0.14
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243201 c.-32G>A upstream_gene_variant 0.11
embB 4248271 c.1760delT frameshift_variant 0.12
ethA 4328387 c.-914A>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0