Run ID: SRR19414522
Sample name:
Date: 03-04-2023 21:37:18
Number of reads: 1742262
Percentage reads mapped: 99.31
Strain: lineage4.1.2.1;lineage3.1.1
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.56 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.36 |
lineage4.1 | Euro-American | T;X;H | None | 0.32 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 0.57 |
lineage4.1.2 | Euro-American | T;H | None | 0.34 |
lineage3.1.1 | East-African-Indian | CAS1-Kili | RD750 | 0.62 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.35 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7792 | p.Thr164Met | missense_variant | 0.43 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.37 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.55 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.37 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.53 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.33 |
rpoB | 761414 | c.1608A>C | synonymous_variant | 0.25 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.61 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.61 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.25 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.57 |
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 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.65 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.72 |
PPE35 | 2170461 | p.Gly51Glu | missense_variant | 0.8 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.64 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.5 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.29 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.57 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fbiB | 3640830 | c.-705C>T | upstream_gene_variant | 0.16 |
rpoA | 3878578 | c.-71C>A | upstream_gene_variant | 0.29 |
embC | 4240172 | p.Val104Met | missense_variant | 0.59 |
embC | 4241562 | p.Arg567His | missense_variant | 0.63 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.65 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.35 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.61 |