Run ID: SRR13583385
Sample name:
Date: 03-04-2023 08:59:16
Number of reads: 2439695
Percentage reads mapped: 99.12
Strain: lineage4.4.1.1;lineage4.3.4.1
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 | 0.53 |
lineage4.4 | Euro-American | S;T | None | 0.41 |
lineage4.4.1 | Euro-American (S-type) | S;T | None | 0.42 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.57 |
lineage4.3.4.1 | Euro-American (LAM) | LAM1;LAM2 | RD174 | 0.55 |
lineage4.4.1.1 | Euro-American | S;Orphans | None | 0.43 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761161 | p.Leu452Pro | missense_variant | 0.67 | rifampicin |
katG | 2155022 | c.1086_1089dupCACC | frameshift_variant | 0.27 | isoniazid |
katG | 2155031 | c.1080delT | frameshift_variant | 0.29 | isoniazid |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.64 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8715 | p.Pro472Ser | missense_variant | 0.66 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoB | 759608 | c.-199C>T | upstream_gene_variant | 0.53 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.56 |
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 | 2102990 | p.Val18Ala | missense_variant | 0.45 |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 0.44 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714914 | c.418delC | frameshift_variant | 0.43 |
ahpC | 2726323 | p.Pro44Arg | missense_variant | 0.43 |
pepQ | 2859830 | p.Gly197Arg | missense_variant | 0.66 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.66 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448598 | p.Ile32Thr | missense_variant | 0.62 |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 0.35 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.59 |
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 0.52 |
Rv3236c | 3612768 | p.Ala117Pro | missense_variant | 0.55 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.54 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.45 |