TB-Profiler result

Run: SRR18003017
Summary

Run ID: SRR18003017

Sample name:

Date: 03-04-2023 19:13:56

Number of reads: 4920198

Percentage reads mapped: 99.18

Strain: lineage4.2.2

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR 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
rpoB 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rpoB 761149 p.Arg448Gln missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4326921 c.552dupC frameshift_variant 0.99 ethionamide
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 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474091 n.434C>T non_coding_transcript_exon_variant 0.67
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.67
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.67
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.5
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.5
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.5
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.5
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.5
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746607 p.Ala331Gly missense_variant 1.0
ribD 2987196 p.Val120Ile missense_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612469 c.648A>G synonymous_variant 1.0
fbiA 3640645 p.Ser35Ala missense_variant 1.0
alr 3841567 c.-147A>G upstream_gene_variant 1.0
clpC1 4039566 p.Val380Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246556 p.Ala15Pro missense_variant 0.11
embB 4246563 p.Leu17Trp missense_variant 0.14
embB 4246567 c.54G>T synonymous_variant 0.17
embB 4247028 p.Leu172Arg missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0