TB-Profiler result

Run: SRR23310991

Summary

Run ID: SRR23310991

Sample name:

Date: 14-03-2023 05:52:21

Number of reads: 1552882

Percentage reads mapped: 99.64

Strain: lineage4.3.4.1;lineage4.1.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.27
lineage4.1 Euro-American T;X;H None 0.68
lineage4.1.2 Euro-American T;H None 0.68
lineage4.3.4 Euro-American (LAM) LAM RD174 0.28
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.7
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.28
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 491591 p.Lys270Met missense_variant 0.5
mshA 575679 p.Asn111Ser missense_variant 0.77
mshA 576616 c.1269G>C synonymous_variant 0.24
rpoB 760106 c.300G>A synonymous_variant 0.52
rpoB 760115 c.309C>T synonymous_variant 0.58
rpoC 763783 c.414G>A synonymous_variant 0.36
rpoC 764995 c.1626C>G synonymous_variant 0.24
rpoC 765150 p.Gly594Glu missense_variant 0.58
rpoC 765325 c.1956C>T synonymous_variant 0.34
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168147 c.2466A>G synonymous_variant 0.27
PPE35 2170065 p.Ala183Gly missense_variant 0.17
Rv1979c 2223123 c.42G>A synonymous_variant 0.41
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.65
folC 2746540 c.1059G>A synonymous_variant 0.41
thyA 3073868 p.Thr202Ala missense_variant 0.37
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fbiD 3339734 p.Ala206Gly missense_variant 0.85
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>C synonymous_variant 0.29
whiB7 3568431 c.249C>G synonymous_variant 0.25
Rv3236c 3612009 p.Ala370Thr missense_variant 0.32
rpoA 3878641 c.-134C>G upstream_gene_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.75
embB 4246529 p.Ser6Arg missense_variant 0.36
embB 4247542 c.1029C>A synonymous_variant 0.62
whiB6 4338513 c.9C>T synonymous_variant 0.64
whiB6 4338550 c.-29A>T upstream_gene_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.17