TB-Profiler result

Run: SRR7517717
Summary

Run ID: SRR7517717

Sample name:

Date: 04-04-2023 19:33:39

Number of reads: 1332615

Percentage reads mapped: 97.74

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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
gyrB 6886 p.Phe549Leu missense_variant 0.25
gyrA 7356 p.Asp19Tyr missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9802 p.Asp834Ala missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491764 p.Leu328Met missense_variant 0.18
ccsA 620346 c.456C>T synonymous_variant 0.2
ccsA 620385 c.495G>T synonymous_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778636 c.-156C>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407170 p.Phe57Leu missense_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.11
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrl 1473743 n.86C>T non_coding_transcript_exon_variant 1.0
rrl 1474602 n.945C>A non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.22
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.22
rrl 1476597 n.2940G>T non_coding_transcript_exon_variant 0.25
fabG1 1673522 p.Gly28Val missense_variant 0.2
inhA 1674696 p.Lys165Asn missense_variant 0.29
inhA 1674785 p.Arg195Leu missense_variant 0.22
rpsA 1833384 c.-158C>A upstream_gene_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154888 p.Phe408Leu missense_variant 0.33
PPE35 2167712 c.2901C>A synonymous_variant 0.22
PPE35 2168284 p.Asp777Tyr missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746786 c.813G>A synonymous_variant 0.4
folC 2746846 c.753C>A synonymous_variant 0.2
folC 2747790 c.-192G>T upstream_gene_variant 0.2
Rv2752c 3064818 c.1374C>A synonymous_variant 0.18
thyX 3067828 p.Gly40Cys missense_variant 0.22
thyX 3067891 p.Ala19Ser missense_variant 0.18
thyA 3074510 c.-39C>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086921 c.102C>A synonymous_variant 0.28
Rv3083 3449164 p.Pro221Ser missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613023 p.Pro32Thr missense_variant 0.17
fbiB 3641546 c.12C>A synonymous_variant 0.22
rpoA 3877772 p.Ser246Pro missense_variant 1.0
rpoA 3878550 c.-43C>A upstream_gene_variant 0.22
rpoA 3878574 c.-67G>T upstream_gene_variant 0.5
clpC1 4039016 c.1689C>A synonymous_variant 0.25
panD 4044114 c.168C>A synonymous_variant 0.24
embC 4240898 p.Leu346Ile missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244810 p.Phe526Leu missense_variant 0.22
embB 4249476 p.Trp988Leu missense_variant 0.2
aftB 4268573 p.Met88Ile missense_variant 0.25
ethA 4326535 c.939G>T synonymous_variant 0.21
whiB6 4338227 p.Ala99Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0