TB-Profiler result

Run: ERR2514666
Summary

Run ID: ERR2514666

Sample name:

Date: 31-03-2023 20:29:35

Number of reads: 3717248

Percentage reads mapped: 96.02

Strain: lineage4.1.1.3.1

Drug-resistance: Pre-XDR-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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 1.0
lineage4.1.1.3.1 Euro-American (X-type) X1;X3 RD193 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
gyrA 7582 p.Asp94Gly missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761277 p.Ile491Phe missense_variant 0.86 rifampicin
pncA 2288956 p.Lys96Glu missense_variant 0.3 pyrazinamide
pncA 2289245 c.-5delG upstream_gene_variant 0.34 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761579 c.1773G>C synonymous_variant 0.13
rpoB 761606 c.1800C>G synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303601 p.Glu224Gly missense_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.17
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.24
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.18
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.18
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.17
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154695 p.Val473Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288845 c.388_396delGTGGTCGGT conservative_inframe_deletion 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877770 c.738A>G synonymous_variant 0.12
rpoA 3877776 c.732T>C synonymous_variant 0.12
rpoA 3877782 c.726T>C synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.99
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4269540 c.-704C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0