TB-Profiler result

Run: SRR3675253

Summary

Run ID: SRR3675253

Sample name:

Date: 04-04-2023 05:24:36

Number of reads: 6486982

Percentage reads mapped: 98.95

Strain: lineage4.3.4.2.1;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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.91
lineage4.1 Euro-American T;X;H None 0.07
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.1
lineage4.3.4 Euro-American (LAM) LAM RD174 0.93
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.08
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.91
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.92
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.29 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.93 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 6140 p.Val301Leu missense_variant 0.96
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.85
rpoC 765150 p.Gly594Glu missense_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781676 c.117C>T synonymous_variant 0.89
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.29
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.12
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.12
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.12
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.12
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.18
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.17
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.17
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.17
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.17
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.15
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.15
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.15
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.15
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.21
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.19
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.11
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.12
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.89
alr 3840719 c.702A>G synonymous_variant 0.96
rpoA 3878626 c.-119A>G upstream_gene_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 0.9
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.92