TB-Profiler result

Run: SRR1169302
Summary

Run ID: SRR1169302

Sample name:

Date: 03-04-2023 02:51:06

Number of reads: 373264

Percentage reads mapped: 97.63

Strain: lineage4.8.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.96
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
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 5298 c.60_61delCG frameshift_variant 0.33
gyrB 5422 p.Tyr61* stop_gained 0.15
gyrB 6364 p.Leu375Phe missense_variant 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 765703 p.Trp778Cys missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460890 c.-155G>A upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472502 n.657G>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673562 p.Lys41Asn missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102647 c.396C>T synonymous_variant 0.22
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289823 c.-582T>C upstream_gene_variant 0.33
pncA 2289877 c.-636C>A upstream_gene_variant 0.33
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
Rv3236c 3612976 c.141C>A synonymous_variant 0.25
fbiB 3642874 p.Leu447Arg missense_variant 1.0
clpC1 4039699 p.Ala336Ser missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247595 p.Cys361Tyr missense_variant 0.38
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0