Run ID: ERR5865744
Sample name:
Date: 02-04-2023 00:14:55
Number of reads: 1932213
Percentage reads mapped: 99.75
Strain: lineage4.3.3
Drug-resistance: MDR-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 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288933 | p.Tyr103* | stop_gained | 1.0 | pyrazinamide |
eis | 2715346 | c.-14C>T | upstream_gene_variant | 1.0 | kanamycin, amikacin |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4326718 | c.754_755dupGC | frameshift_variant | 1.0 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 1.0 |
gyrA | 9209 | p.Lys636Asn | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
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 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.11 |
fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.11 |
fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.11 |
fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.11 |
rpsA | 1834836 | p.Met432Thr | missense_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.33 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.37 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 |
folC | 2746340 | p.Ala420Val | missense_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
clpC1 | 4038968 | c.1737G>A | synonymous_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.13 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.19 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.19 |
gid | 4407843 | p.Glu120Asp | missense_variant | 0.25 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |
whiB6 | 4338458 | c.-2974_63del | start_lost&conservative_inframe_deletion | 1.0 |