TB-Profiler result

Run: SRR2101429

Summary

Run ID: SRR2101429

Sample name:

Date: 03-04-2023 23:42:41

Number of reads: 547309

Percentage reads mapped: 99.78

Strain: lineage4.3.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576134 p.Val263Phe missense_variant 0.14
mshA 576298 p.Asp317Glu missense_variant 0.13
ccsA 620748 c.858T>G synonymous_variant 0.21
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303055 p.Asp42Gly missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473693 n.36G>A non_coding_transcript_exon_variant 0.11
rrl 1474378 n.721G>A non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168100 c.2512delC frameshift_variant 0.15
PPE35 2170013 c.600C>A synonymous_variant 0.25
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289793 c.-552C>T upstream_gene_variant 0.12
kasA 2518147 c.33C>T synonymous_variant 0.3
kasA 2518593 p.Ala160Asp missense_variant 0.15
kasA 2519057 p.Thr315Ser missense_variant 0.11
kasA 2519062 c.948T>G synonymous_variant 0.11
kasA 2519065 c.951C>A synonymous_variant 0.11
kasA 2519070 p.Asp319Val missense_variant 0.11
Rv2752c 3066318 c.-127C>G upstream_gene_variant 0.11
thyX 3067973 c.-28A>G upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612161 p.Ala319Glu missense_variant 0.11
fbiB 3642684 c.1150T>C synonymous_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044075 c.207T>A synonymous_variant 0.14
embC 4240648 c.786C>T synonymous_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244036 c.804C>A synonymous_variant 0.12
embA 4244464 p.Ala411Asp missense_variant 0.5
embB 4246920 p.Pro136Leu missense_variant 0.18
embB 4248857 p.Gly782* stop_gained 0.11
embB 4249528 c.3015C>T synonymous_variant 0.1
ethA 4327213 p.Ser87Arg missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0