TB-Profiler result

Run: SRR4034800
Summary

Run ID: SRR4034800

Sample name:

Date: 04-04-2023 07:05:06

Number of reads: 138366

Percentage reads mapped: 99.6

Strain: lineage4.9;lineage4.1.1

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
lineage4.9 Euro-American (H37Rv-like) T1 None 0.81
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.11
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
tlyA 1918074 c.138_139delGT frameshift_variant 1.0 capreomycin
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 6003 c.765delT frameshift_variant 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
fbiC 1303825 p.Glu299Lys missense_variant 0.33
fbiC 1304045 p.Pro372His missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918520 p.Pro194Arg missense_variant 0.67
Rv1979c 2221740 c.1425C>T synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289464 c.-223A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612693 p.Arg142Trp missense_variant 0.67
fbiA 3641447 p.Thr302Met missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 1.0
clpC1 4038245 c.2460C>T synonymous_variant 1.0
embC 4240293 p.Leu144Pro missense_variant 0.67
embC 4240793 p.Ala311Thr missense_variant 0.67
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241355 p.Gln498Arg missense_variant 0.25
embC 4241655 p.Gly598Glu missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242751 c.-482G>A upstream_gene_variant 0.67
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245327 p.Ala699Thr missense_variant 0.67
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0