TB-Profiler result

Run: SRR6982331
Summary

Run ID: SRR6982331

Sample name:

Date: 04-04-2023 18:34:21

Number of reads: 1135972

Percentage reads mapped: 99.27

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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
ccsA 619706 c.-185G>A upstream_gene_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767032 c.3663G>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777206 c.1275A>G synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
fbiC 1303091 p.Glu54Gly missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474048 n.391G>A non_coding_transcript_exon_variant 1.0
rrl 1476789 n.3132T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170011 p.Arg201Leu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289846 c.-605C>G upstream_gene_variant 0.1
folC 2746346 p.Ala418Val missense_variant 0.1
folC 2746627 p.Asp324Glu missense_variant 0.11
thyA 3074648 c.-177T>G upstream_gene_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475298 p.Arg431Gln missense_variant 0.1
Rv3236c 3612212 p.Ala302Val missense_variant 0.11
Rv3236c 3612515 p.Arg201His missense_variant 0.11
fbiB 3642775 p.Leu414Pro missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0