TB-Profiler result

Run: SRR13837495
Summary

Run ID: SRR13837495

Sample name:

Date: 03-04-2023 09:11:44

Number of reads: 591072

Percentage reads mapped: 95.55

Strain: lineage4.9

Drug-resistance: Other

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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
lineage4.9 Euro-American (H37Rv-like) T1 None 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
ethA 4327340 p.Trp45* stop_gained 1.0 ethionamide
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 8646 p.Gln449Lys missense_variant 1.0
gyrA 9138 p.Gln613Lys missense_variant 0.96
gyrA 9604 p.Val768Ala missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 1.0
rpoB 761853 p.Ile683Val missense_variant 1.0
rpoC 764524 c.1155C>G synonymous_variant 0.11
rpoC 767119 c.3750A>G synonymous_variant 0.11
rpoC 767158 c.3789T>C synonymous_variant 0.11
mmpL5 777509 c.972G>T synonymous_variant 1.0
mmpS5 779508 c.-603G>C upstream_gene_variant 1.0
Rv1258c 1406904 c.436dupT frameshift_variant 1.0
Rv1258c 1407127 p.Arg72Ser missense_variant 1.0
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.96
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
inhA 1674552 c.351C>G synonymous_variant 1.0
rpsA 1834079 p.Arg180Cys missense_variant 1.0
PPE35 2168448 p.Gln722Pro missense_variant 1.0
Rv1979c 2221876 p.Val430Glu missense_variant 1.0
kasA 2518036 c.-78delG upstream_gene_variant 1.0
kasA 2518088 c.-27T>A upstream_gene_variant 1.0
eis 2714449 p.Trp295Ser missense_variant 1.0
eis 2714773 p.Pro187Gln missense_variant 1.0
eis 2715525 c.-193G>T upstream_gene_variant 1.0
ahpC 2726611 c.419_420insA frameshift_variant 1.0
folC 2747455 c.144C>A synonymous_variant 1.0
pepQ 2859723 c.696T>C synonymous_variant 1.0
ribD 2987540 c.702G>T synonymous_variant 1.0
fbiD 3339321 c.204G>A synonymous_variant 1.0
fprA 3474339 p.Met111Ile missense_variant 1.0
fprA 3474353 c.348delT frameshift_variant 1.0
rpoA 3877677 c.831G>C synonymous_variant 0.1
rpoA 3877692 c.816G>C synonymous_variant 0.11
clpC1 4038436 p.Ala757Ser missense_variant 1.0
embC 4242635 p.Ala925Ser missense_variant 1.0
embB 4249145 c.2634delC frameshift_variant 1.0
ubiA 4269803 p.Ala11Pro missense_variant 1.0
ethA 4326689 p.Lys262Thr missense_variant 1.0
ethA 4326849 p.Pro209Thr missense_variant 1.0