Run ID: ERR3148151
Sample name:
Date: 15-08-2022 11:50:54
Number of reads: 358994
Percentage reads mapped: 99.37
Strain: lineage4.1.1.3
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 |
lineage4.1 | Euro-American | T;X;H | None | 1.0 |
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 |
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 | 2288883 | p.Leu120Pro | missense_variant | 1.0 | pyrazinamide |
pncA | 2289067 | p.Ser59Pro | missense_variant | 0.13 | pyrazinamide |
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 |
rpoB | 761079 | p.Phe425Leu | missense_variant | 0.12 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 766487 | p.Pro1040Ser | missense_variant | 1.0 |
mmpL5 | 776668 | p.Asp605Tyr | missense_variant | 0.15 |
mmpS5 | 779534 | c.-629C>A | upstream_gene_variant | 0.14 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302884 | c.-47T>C | upstream_gene_variant | 0.11 |
Rv1258c | 1406344 | p.Asn333Tyr | missense_variant | 0.15 |
Rv1258c | 1406794 | c.547T>C | synonymous_variant | 0.14 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1473053 | n.1208T>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473062 | n.1217T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473304 | n.1459C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476610 | n.2953C>T | non_coding_transcript_exon_variant | 0.14 |
rpsA | 1833727 | c.186G>A | synonymous_variant | 1.0 |
PPE35 | 2169632 | c.981C>A | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289729 | c.-488C>T | upstream_gene_variant | 0.2 |
kasA | 2518147 | c.33C>T | synonymous_variant | 0.3 |
eis | 2714150 | p.Pro395Thr | missense_variant | 0.11 |
folC | 2746685 | p.Ala305Val | missense_variant | 0.2 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612897 | p.Gly74Ser | missense_variant | 0.2 |
fbiA | 3641315 | p.Thr258Met | missense_variant | 0.1 |
fbiB | 3641859 | p.Asp109Tyr | missense_variant | 0.14 |
fbiB | 3641902 | p.Val123Ala | missense_variant | 0.14 |
alr | 3841353 | p.Leu23* | stop_gained | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embA | 4244340 | p.Ser370Pro | missense_variant | 0.12 |
embB | 4247042 | p.Pro177Ser | missense_variant | 0.12 |
embB | 4247249 | p.Gly246Cys | missense_variant | 0.14 |
embB | 4247498 | p.Pro329Thr | missense_variant | 0.14 |
ethA | 4326900 | p.Pro192Thr | missense_variant | 1.0 |
whiB6 | 4338197 | p.His109Asn | missense_variant | 0.11 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |