TB-Profiler result

Run: ERR221637
Summary

Run ID: ERR221637

Sample name:

Date: 31-03-2023 16:19:41

Number of reads: 6963229

Percentage reads mapped: 99.36

Strain: lineage4;lineage3.1.2

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 0.94
lineage4 Euro-American LAM;T;S;X;H None 0.06
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.9
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.94
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 491742 c.960T>C synonymous_variant 0.95
rpoB 759746 c.-61C>T upstream_gene_variant 0.95
rpoC 762434 c.-936T>G upstream_gene_variant 0.93
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.91
katG 2156066 p.Ala16Thr missense_variant 0.93
PPE35 2167926 p.Leu896Ser missense_variant 0.9
PPE35 2168604 p.Pro670Leu missense_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.94
pncA 2289365 c.-125delC upstream_gene_variant 0.94
eis 2714424 c.909C>T synonymous_variant 0.96
ahpC 2726105 c.-88G>A upstream_gene_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.21
embC 4242075 p.Arg738Gln missense_variant 0.96
embC 4242425 p.Arg855Gly missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4327427 p.Gly16Ala missense_variant 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.93