Run ID: SRR23310991
Sample name:
Date: 14-03-2023 05:52:21
Number of reads: 1552882
Percentage reads mapped: 99.64
Strain: lineage4.3.4.1;lineage4.1.2.1
Drug-resistance: Sensitive
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 | 0.27 |
lineage4.1 | Euro-American | T;X;H | None | 0.68 |
lineage4.1.2 | Euro-American | T;H | None | 0.68 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.28 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.7 |
lineage4.3.4.1 | Euro-American (LAM) | LAM1;LAM2 | RD174 | 0.28 |
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 | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.5 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.77 |
mshA | 576616 | c.1269G>C | synonymous_variant | 0.24 |
rpoB | 760106 | c.300G>A | synonymous_variant | 0.52 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.58 |
rpoC | 763783 | c.414G>A | synonymous_variant | 0.36 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.24 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.58 |
rpoC | 765325 | c.1956C>T | synonymous_variant | 0.34 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.98 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
fabG1 | 1673553 | p.Asp38Glu | missense_variant | 0.24 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168147 | c.2466A>G | synonymous_variant | 0.27 |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.17 |
Rv1979c | 2223123 | c.42G>A | synonymous_variant | 0.41 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.65 |
folC | 2746540 | c.1059G>A | synonymous_variant | 0.41 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.37 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.98 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.85 |
fprA | 3473996 | c.-10_-9insA | upstream_gene_variant | 1.0 |
whiB7 | 3568428 | c.252A>C | synonymous_variant | 0.29 |
whiB7 | 3568431 | c.249C>G | synonymous_variant | 0.25 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.32 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.25 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.18 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.75 |
embB | 4246529 | p.Ser6Arg | missense_variant | 0.36 |
embB | 4247542 | c.1029C>A | synonymous_variant | 0.62 |
whiB6 | 4338513 | c.9C>T | synonymous_variant | 0.64 |
whiB6 | 4338550 | c.-29A>T | upstream_gene_variant | 0.23 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.17 |