Run ID: ERR5530521
Sample name:
Date: 01-04-2023 22:33:38
Number of reads: 4776901
Percentage reads mapped: 99.71
Strain: lineage4.3.4.1
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 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 1.0 |
lineage4.3.4.1 | Euro-American (LAM) | LAM1;LAM2 | RD174 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289067 | p.Ser59Pro | missense_variant | 1.0 | pyrazinamide |
embB | 4247730 | p.Gly406Asp | missense_variant | 1.0 | ethambutol |
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 |
gyrA | 9315 | c.2014C>T | synonymous_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.23 |
mshA | 576613 | c.1266A>C | synonymous_variant | 0.31 |
mshA | 576616 | c.1269G>C | synonymous_variant | 0.22 |
rpoB | 762793 | p.Val996Ala | missense_variant | 0.13 |
rpoC | 764367 | p.Gly333Ala | missense_variant | 0.2 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
rpoC | 767123 | p.Val1252Leu | 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 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102307 | p.Gly246Ser | missense_variant | 1.0 |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.25 |
Rv1979c | 2222854 | p.Ile104Thr | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.21 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.53 |
fbiD | 3339751 | p.Ala212Pro | missense_variant | 0.2 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
clpC1 | 4039991 | c.714G>A | synonymous_variant | 1.0 |
embC | 4240409 | p.Pro183Ala | missense_variant | 0.25 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246527 | p.Ala5Gly | missense_variant | 0.21 |
embB | 4247723 | p.Pro404Ala | missense_variant | 1.0 |
embB | 4248328 | c.1815G>C | synonymous_variant | 0.23 |
whiB6 | 4338440 | c.81dupT | frameshift_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |