TB-Profiler result

Run: ERR2513895

Summary

Run ID: ERR2513895

Sample name:

Date: 31-03-2023 19:58:38

Number of reads: 682060

Percentage reads mapped: 99.66

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 8855 c.1554C>T synonymous_variant 0.13
mshA 576188 p.Asp281Asn missense_variant 0.2
ccsA 619831 c.-60T>G upstream_gene_variant 0.33
rpoB 762480 p.Ile892Val missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.15
mmpL5 777128 c.1353A>G synonymous_variant 0.12
mmpL5 777580 p.Thr301Ser missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 0.88
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101923 p.Ser374Pro missense_variant 0.15
PPE35 2167745 p.Thr956Arg missense_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.13
PPE35 2169269 c.1344A>G synonymous_variant 0.23
PPE35 2169272 c.1341C>G synonymous_variant 0.26
PPE35 2169278 c.1335T>C synonymous_variant 0.25
PPE35 2169281 c.1332T>G synonymous_variant 0.25
PPE35 2169287 c.1326T>C synonymous_variant 0.21
PPE35 2169293 c.1320T>C synonymous_variant 0.12
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.39
PPE35 2170053 p.Thr187Ser missense_variant 0.39
PPE35 2170392 p.Gly74Ala missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.16
kasA 2519140 c.1026G>C synonymous_variant 0.12
kasA 2519143 c.1029G>C synonymous_variant 0.12
kasA 2519153 p.Ile347Val missense_variant 0.13
folC 2746735 c.864C>T synonymous_variant 0.25
folC 2746857 p.Glu248Lys missense_variant 0.14
pepQ 2859832 p.Ala196Gly missense_variant 0.17
ribD 2987588 p.Tyr250* stop_gained 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.31
ddn 3987268 p.Arg142Pro missense_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246151 c.-363A>G upstream_gene_variant 1.0
embB 4246637 p.Val42Leu missense_variant 1.0
ethR 4326961 c.-588G>C upstream_gene_variant 0.16
ethR 4326964 c.-585G>A upstream_gene_variant 0.16
ethR 4326970 c.-579G>T upstream_gene_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>G upstream_gene_variant 0.62
whiB6 4338602 c.-81A>T upstream_gene_variant 0.62
whiB6 4338610 c.-89G>A upstream_gene_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0