TB-Profiler result

Run: SRR19428599
Summary

Run ID: SRR19428599

Sample name:

Date: 03-04-2023 21:41:58

Number of reads: 814557

Percentage reads mapped: 99.48

Strain: lineage4.1.1.3

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
lineage4.1.1 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
katG 2153932 p.Ala727Asp missense_variant 0.12 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
gyrB 5723 p.Ala162Ser missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7757 p.Phe152Leu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762345 p.Phe847Leu missense_variant 0.11
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473827 n.170G>T non_coding_transcript_exon_variant 0.11
rrl 1473859 n.202T>C non_coding_transcript_exon_variant 0.13
rrl 1473906 n.249G>C non_coding_transcript_exon_variant 0.15
rrl 1473925 n.268G>T non_coding_transcript_exon_variant 0.14
rrl 1475030 n.1373G>T non_coding_transcript_exon_variant 0.12
rrl 1475101 n.1444T>C non_coding_transcript_exon_variant 0.1
rrl 1475232 n.1575A>G non_coding_transcript_exon_variant 0.12
rrl 1475684 n.2027G>C non_coding_transcript_exon_variant 0.11
rrl 1476220 n.2563G>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168810 c.1803T>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.16
Rv1979c 2222272 p.Ala298Asp missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064564 c.1627delG frameshift_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474045 c.39G>T synonymous_variant 0.15
fprA 3474048 c.42G>A synonymous_variant 0.15
fprA 3474053 c.48_51delCTTC frameshift_variant 0.17
fprA 3474065 c.60_68delATCCTTGCT disruptive_inframe_deletion 0.17
fprA 3474079 p.Ala25Asn missense_variant 0.18
fbiB 3642027 p.Val165Leu missense_variant 0.1
rpoA 3877760 p.Pro250Thr missense_variant 0.11
rpoA 3878505 c.3G>C start_lost 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243697 p.Ile155Met missense_variant 1.0
embB 4247941 c.1428G>A synonymous_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0