TB-Profiler result

Run: SRR6044976
Summary

Run ID: SRR6044976

Sample name:

Date: 04-04-2023 11:50:31

Number of reads: 219331

Percentage reads mapped: 98.81

Strain: lineage4.9;lineage3

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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 0.19
lineage4 Euro-American LAM;T;S;X;H None 0.95
lineage4.9 Euro-American (H37Rv-like) T1 None 0.88
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 9304 p.Gly668Asp missense_variant 1.0
mshA 576221 p.Gly292Arg missense_variant 1.0
ccsA 620502 c.612T>G synonymous_variant 0.33
rpoB 759746 c.-61C>T upstream_gene_variant 0.75
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 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778835 p.Thr24Met missense_variant 1.0
mmpS5 778941 c.-36A>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800901 c.96dupG frameshift_variant 0.4
embR 1417407 c.-60C>A upstream_gene_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833916 c.375C>G synonymous_variant 0.4
rpsA 1834183 c.642T>G synonymous_variant 0.4
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
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840519 c.901dupG frameshift_variant 0.33
ddn 3986999 c.158dupG frameshift_variant 0.67
embC 4242075 p.Arg738Gln missense_variant 1.0
ethA 4328364 c.-891C>A upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0