TB-Profiler result

Run: SRR12142330
Summary

Run ID: SRR12142330

Sample name:

Date: 03-04-2023 06:16:43

Number of reads: 8758546

Percentage reads mapped: 99.35

Strain: lineage4.4.2

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 None 0.99
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
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7691 c.390C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491246 p.Tyr155Cys missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777750 p.Arg244His missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.18
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.18
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.18
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.18
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.17
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.17
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.17
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.17
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.15
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.14
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.14
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.14
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.13
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.13
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.14
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223039 c.126C>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841232 c.189G>A synonymous_variant 1.0
clpC1 4038884 c.1821C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 0.99
aftB 4269375 c.-539G>A upstream_gene_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0