Run ID: ERR9907755
Sample name:
Date: 02-04-2023 13:39:14
Number of reads: 2847669
Percentage reads mapped: 99.36
Strain: lineage4.8.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
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 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6734 | p.Asn499Asp | missense_variant | 0.32 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7581 | p.Asp94Tyr | missense_variant | 0.42 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288704 | p.Val180Phe | missense_variant | 1.0 | pyrazinamide |
embA | 4243222 | c.-11C>A | upstream_gene_variant | 1.0 | ethambutol |
ethA | 4327132 | c.341delA | frameshift_variant | 1.0 | ethionamide, ethionamide |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 8467 | p.His389Pro | missense_variant | 0.2 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.18 |
rpoB | 759939 | p.Pro45Ser | missense_variant | 1.0 |
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 | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.23 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.2 |
ald | 3087818 | p.Cys333Trp | missense_variant | 0.15 |
fbiD | 3339040 | c.-78T>C | upstream_gene_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.38 |
fbiB | 3642874 | p.Leu447Arg | missense_variant | 1.0 |
rpoA | 3878613 | c.-106A>C | upstream_gene_variant | 0.25 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.37 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.21 |
embB | 4248324 | p.Ala604Gly | missense_variant | 0.24 |
embB | 4248328 | c.1815G>C | synonymous_variant | 0.18 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |