TB-Profiler result

Run: ERR2514632
Summary

Run ID: ERR2514632

Sample name:

Date: 31-03-2023 20:28:35

Number of reads: 6484894

Percentage reads mapped: 99.58

Strain: lineage3.1.2.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.1 East-African-Indian CAS2 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407965 p.Ala80Pro missense_variant 1.0 streptomycin
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 491742 c.960T>C synonymous_variant 1.0
mshA 576628 c.1281G>T synonymous_variant 0.67
ccsA 619695 c.-196G>A upstream_gene_variant 0.15
ccsA 619968 c.78G>A synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.99
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.97
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304063 p.Ala378Val missense_variant 0.57
fbiC 1304291 p.Asp454Gly missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918119 c.180C>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
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 2714993 p.Pro114Ser missense_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2987308 p.Ala157Glu missense_variant 0.12
Rv2752c 3065196 c.996T>C synonymous_variant 1.0
ald 3086771 c.-49T>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339344 p.Gly76Asp missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642173 c.639G>A synonymous_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242541 c.-692C>T upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243625 c.393C>T synonymous_variant 0.22
embA 4243870 p.Ala213Val missense_variant 0.12
embA 4244380 c.1149delG frameshift_variant 0.2
embA 4245753 p.Gly841Ser missense_variant 0.29
embB 4247042 p.Pro177Ser missense_variant 0.25
ubiA 4270033 c.-201delG upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0