TB-Profiler result

Run: SRR6896346
Summary

Run ID: SRR6896346

Sample name:

Date: 04-04-2023 18:03:08

Number of reads: 513326

Percentage reads mapped: 99.55

Strain: lineage4.1.2

Drug-resistance: HR-TB

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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
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
katG 2155168 p.Ser315Thr missense_variant 0.42 isoniazid
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 7580 c.279C>T synonymous_variant 0.55
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8086 p.Asp262Val missense_variant 0.3
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.75
mshA 575164 c.-184T>A upstream_gene_variant 0.11
mshA 575679 p.Asn111Ser missense_variant 0.86
rpoB 760115 c.309C>T synonymous_variant 0.72
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407344 c.-4A>G upstream_gene_variant 0.1
embR 1417140 p.Ala70Ser missense_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473847 n.190G>T non_coding_transcript_exon_variant 0.11
rrl 1473926 n.269G>T non_coding_transcript_exon_variant 0.11
rrl 1474739 n.1082G>T non_coding_transcript_exon_variant 0.18
fabG1 1673249 c.-191C>T upstream_gene_variant 0.3
inhA 1674498 c.297G>C synonymous_variant 0.79
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918451 p.Ala171Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289843 c.-602T>C upstream_gene_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 0.66
folC 2747022 p.Val193Ile missense_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448894 p.Tyr131Asp missense_variant 0.33
Rv3083 3449642 p.Asn380Ser missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641164 p.Ile208Val missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4242838 c.-395C>T upstream_gene_variant 0.17
embA 4244581 p.Asp450Val missense_variant 0.12
embA 4245344 c.2112G>A synonymous_variant 0.15
embB 4249428 p.Arg972Leu missense_variant 0.12
embB 4249709 p.Lys1066Glu missense_variant 0.29
aftB 4268238 p.Met200Thr missense_variant 0.12
aftB 4268861 c.-25T>C upstream_gene_variant 0.35
aftB 4269129 c.-293G>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0