TB-Profiler result

Run: SRR2101462
Summary

Run ID: SRR2101462

Sample name:

Date: 03-04-2023 23:44:02

Number of reads: 490939

Percentage reads mapped: 96.71

Strain: lineage4.9

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 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
pncA 2289224 p.Ile6Met missense_variant 0.12 pyrazinamide
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
fgd1 490901 c.123delT frameshift_variant 0.12
mshA 575761 c.414C>T synonymous_variant 1.0
mshA 576004 c.657T>C synonymous_variant 0.12
rpoB 759814 p.Asp3Gly missense_variant 1.0
rpoC 764780 c.1411_1412delAGinsTC synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779349 c.-869C>A upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781502 c.-58G>T upstream_gene_variant 1.0
fbiC 1304534 p.Leu535Ser missense_variant 0.12
embR 1416772 c.576C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.13
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.13
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.13
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.13
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.13
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.13
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.13
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.13
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.12
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.12
rpsA 1833372 c.-170C>T upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169044 c.1569G>C synonymous_variant 0.5
PPE35 2169047 p.Ile522Val missense_variant 0.33
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 0.33
PPE35 2169059 c.1554G>A synonymous_variant 0.67
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169065 p.Ala516Ile missense_variant 0.67
PPE35 2169068 c.1545G>T synonymous_variant 0.57
PPE35 2169071 c.1542A>G synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289166 p.Ala26Ser missense_variant 0.12
fbiB 3642772 p.Asp413Ala missense_variant 0.4
embB 4249591 p.Asp1026Glu missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0