TB-Profiler result

Run: SRR6982265
Summary

Run ID: SRR6982265

Sample name:

Date: 04-04-2023 18:32:17

Number of reads: 270431

Percentage reads mapped: 98.01

Strain: lineage4.9

Drug-resistance: RR-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
lineage4.9 Euro-American (H37Rv-like) T1 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
rpoB 761116 p.Asn437Ser missense_variant 0.11 rifampicin
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 6533 p.Ala432Ser missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8337 p.Leu346Ile missense_variant 0.12
mshA 575159 c.-189C>T upstream_gene_variant 0.2
mshA 576478 c.1131G>A synonymous_variant 1.0
rpoB 761190 p.Ala462Thr missense_variant 0.12
rpoB 761331 p.Pro509Thr missense_variant 0.1
rpoB 761820 p.Ser672Thr missense_variant 0.13
rpoC 764827 c.1458G>A synonymous_variant 0.15
rpsL 781424 c.-136T>C upstream_gene_variant 0.17
rpsL 781870 p.Thr104Met missense_variant 0.12
fbiC 1303250 p.Phe107Tyr missense_variant 0.12
fbiC 1304219 p.Pro430Gln missense_variant 0.12
fbiC 1304236 p.Gln436Lys missense_variant 0.13
embR 1417110 p.Arg80Gly missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473934 n.277G>C non_coding_transcript_exon_variant 0.17
rrl 1474926 n.1269C>A non_coding_transcript_exon_variant 0.12
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.17
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.15
rrl 1476715 n.3058A>T non_coding_transcript_exon_variant 0.12
inhA 1673763 c.-439C>T upstream_gene_variant 0.11
rpsA 1834611 p.Arg357Leu missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102934 p.Asp37Tyr missense_variant 0.17
ndh 2103101 c.-59C>A upstream_gene_variant 0.17
katG 2154765 c.1347C>A synonymous_variant 0.15
katG 2154825 c.1287G>T synonymous_variant 0.13
PPE35 2170083 p.Gly177Val missense_variant 0.22
kasA 2518335 p.Arg74Leu missense_variant 0.18
eis 2715492 c.-160G>T upstream_gene_variant 0.14
ahpC 2726201 c.9G>T synonymous_variant 0.17
pepQ 2859963 c.456C>A synonymous_variant 0.18
pepQ 2860022 p.Glu133* stop_gained 0.14
ribD 2986775 c.-64A>T upstream_gene_variant 0.12
ribD 2986943 c.105G>A synonymous_variant 0.13
Rv2752c 3066354 c.-163G>A upstream_gene_variant 0.2
Rv3236c 3612085 c.1032C>A synonymous_variant 0.18
fbiB 3642414 p.Pro294Thr missense_variant 0.4
embA 4243390 p.Gly53Val missense_variant 0.15
embB 4246137 c.-377C>A upstream_gene_variant 0.22
embB 4248436 c.1923C>G synonymous_variant 0.12
embB 4249447 c.2934G>T synonymous_variant 0.18
ethA 4327436 p.Gly13Val missense_variant 0.18
whiB6 4338594 c.-74delC upstream_gene_variant 1.0