TB-Profiler result

Run: SRR1173765
Summary

Run ID: SRR1173765

Sample name:

Date: 03-04-2023 03:31:14

Number of reads: 1252872

Percentage reads mapped: 97.34

Strain: lineage4.1.2.1

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
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.99
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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
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 7930 p.Ala210Val missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620064 c.174C>T synonymous_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761189 c.1383T>G synonymous_variant 0.11
rpoB 761192 c.1386C>G synonymous_variant 0.11
rpoB 761195 c.1389G>C synonymous_variant 0.12
rpoB 761198 c.1392G>C synonymous_variant 0.11
rpoB 761414 c.1608A>G synonymous_variant 0.1
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.95
mmpR5 779407 c.421dupG frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155270 p.Ala281Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726765 c.573C>A synonymous_variant 0.12
Rv2752c 3066006 c.186G>T synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640415 c.-128T>C upstream_gene_variant 1.0
clpC1 4040070 p.Pro212Gln missense_variant 0.11
clpC1 4040085 p.Arg207Leu missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4269804 c.-968G>C upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0