Run ID: ERR2660417
Sample name:
Date: 31-03-2023 22:46:56
Number of reads: 3207027
Percentage reads mapped: 99.59
Strain: lineage4.3.4.2.1;lineage1.2.2.2
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.61 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.43 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.58 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 0.44 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.56 |
lineage1.2.2.2 | Indo-Oceanic | NA | RD239 | 0.46 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 0.6 |
lineage4.3.4.2.1 | Euro-American (LAM) | LAM11 | RD174 | 0.58 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 0.44 |
gyrB | 6112 | p.Met291Ile | missense_variant | 0.4 |
gyrB | 6140 | p.Val301Leu | missense_variant | 0.62 |
gyrA | 7268 | c.-34C>T | upstream_gene_variant | 0.39 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.39 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.41 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.39 |
rpoB | 762731 | p.Gln975His | missense_variant | 0.39 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.38 |
rpoC | 763552 | c.183C>T | synonymous_variant | 0.34 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.43 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.41 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.65 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.37 |
mmpS5 | 779625 | c.-720G>A | upstream_gene_variant | 0.42 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.44 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1833760 | c.219C>T | synonymous_variant | 0.69 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102240 | p.Arg268His | missense_variant | 0.34 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.48 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.47 |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.46 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.4 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.45 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.43 |
thyX | 3067248 | p.Thr233Ile | missense_variant | 0.66 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.54 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.45 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.44 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.52 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.65 |
alr | 3840719 | c.702A>G | synonymous_variant | 0.59 |
alr | 3841525 | c.-105G>T | upstream_gene_variant | 0.42 |
rpoA | 3878578 | c.-71C>A | upstream_gene_variant | 0.33 |
rpoA | 3878639 | c.-132C>G | upstream_gene_variant | 0.15 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.55 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.42 |
clpC1 | 4040719 | c.-15A>G | upstream_gene_variant | 0.41 |
embC | 4240162 | c.300C>T | synonymous_variant | 0.41 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.33 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.35 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245670 | p.Ala813Gly | missense_variant | 0.39 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.43 |
embB | 4246979 | p.Gly156Cys | missense_variant | 0.45 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.44 |
aftB | 4267960 | p.Val293Met | missense_variant | 0.41 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.46 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.39 |
ethA | 4326148 | c.1326G>T | synonymous_variant | 0.39 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.41 |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.47 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.35 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.35 |
gid | 4407848 | p.Ala119Thr | missense_variant | 0.41 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.43 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.57 |