TB-Profiler result

Run: SRR1172260
Summary

Run ID: SRR1172260

Sample name:

Date: 03-04-2023 03:01:26

Number of reads: 866098

Percentage reads mapped: 98.52

Strain: lineage4.8.1

Drug-resistance: MDR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288790 p.Leu151Ser missense_variant 1.0 pyrazinamide
embB 4247729 p.Gly406Cys missense_variant 1.0 ethambutol
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 6619 c.-683T>C upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 765719 p.Glu784Gln missense_variant 0.1
mmpL5 775631 p.Gln950His missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407185 p.Met52Ile missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473703 n.46C>A non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.1
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.1
rrl 1476603 n.2946G>T non_coding_transcript_exon_variant 0.1
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.11
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.11
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.11
tlyA 1917776 c.-164G>T upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918454 p.Ser172Leu missense_variant 0.12
katG 2155367 p.Arg249Ser missense_variant 0.11
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746375 c.1224G>A synonymous_variant 0.15
ald 3087737 c.918G>C synonymous_variant 0.13
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612581 p.Leu179Pro missense_variant 0.12
fbiB 3642874 p.Leu447Arg missense_variant 1.0
rpoA 3878569 c.-62C>G upstream_gene_variant 0.5
rpoA 3878574 c.-67G>C upstream_gene_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448500 c.-3_*1408del transcript_ablation 1.0