Run ID: SRR6896288
Sample name:
Date: 04-04-2023 18:01:21
Number of reads: 888469
Percentage reads mapped: 98.28
Strain: lineage4.3.2.1
Drug-resistance: RR-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 |
lineage4.3.2 | Euro-American (LAM) | LAM3 | None | 1.0 |
lineage4.3.2.1 | Euro-American (LAM) | LAM3 | RD761 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761196 | p.Leu464Met | missense_variant | 0.11 | rifampicin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5520 | p.Pro94Leu | missense_variant | 1.0 |
gyrA | 7222 | c.-80C>T | upstream_gene_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 576751 | p.Lys468Asn | missense_variant | 0.22 |
rpoB | 759620 | c.-187A>C | upstream_gene_variant | 0.23 |
rpoB | 761147 | c.1341C>T | synonymous_variant | 0.1 |
rpoB | 761162 | c.1356G>C | synonymous_variant | 0.1 |
rpoB | 761174 | c.1368T>C | synonymous_variant | 0.11 |
rpoB | 761180 | c.1374A>C | synonymous_variant | 0.11 |
rpoB | 761183 | c.1377T>C | synonymous_variant | 0.11 |
rpoB | 761186 | p.Glu460Asp | missense_variant | 0.11 |
rpoB | 761195 | c.1389G>C | synonymous_variant | 0.11 |
rpoB | 761213 | c.1407G>C | synonymous_variant | 0.1 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1407475 | c.-135G>T | upstream_gene_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 0.92 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476337 | n.2680C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154570 | c.1542G>A | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290107 | c.-866T>A | upstream_gene_variant | 1.0 |
ahpC | 2726338 | p.Val49Gly | missense_variant | 0.25 |
Rv2752c | 3066199 | c.-8G>T | upstream_gene_variant | 0.11 |
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 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244860 | p.Gly543Val | missense_variant | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |