Run ID: ERR161123
Sample name:
Date: 31-03-2023 14:47:00
Number of reads: 4179442
Percentage reads mapped: 99.36
Strain: lineage4.3.4.2.1;lineage1.2.2.1
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.18 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.82 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.19 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 0.85 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.18 |
lineage1.2.2.1 | Indo-Oceanic | NA | RD239 | 0.81 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 0.17 |
lineage4.3.4.2.1 | Euro-American (LAM) | LAM11 | RD174 | 0.19 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 0.84 |
gyrB | 6112 | p.Met291Ile | missense_variant | 0.72 |
gyrB | 6140 | p.Val301Leu | missense_variant | 0.28 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.79 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.86 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491060 | p.Met93Thr | missense_variant | 0.81 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.8 |
ccsA | 620659 | p.Arg257Cys | missense_variant | 0.79 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.83 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.79 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.79 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.19 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.82 |
mmpL5 | 776311 | p.Gly724Ser | missense_variant | 0.13 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800899 | p.Ala31Thr | missense_variant | 0.89 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.85 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471842 | n.-4T>G | upstream_gene_variant | 0.83 |
rrl | 1474517 | n.860C>T | non_coding_transcript_exon_variant | 0.8 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.77 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.98 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.25 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.23 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.78 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.82 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.77 |
Rv2752c | 3064761 | c.1431C>T | synonymous_variant | 0.15 |
Rv2752c | 3064852 | p.Met447Thr | missense_variant | 0.77 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.26 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.22 |
thyA | 3074553 | c.-82C>T | upstream_gene_variant | 0.14 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339153 | p.Leu12Phe | missense_variant | 0.23 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.78 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.91 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.76 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.17 |
Rv3236c | 3612865 | p.Ser84Arg | missense_variant | 0.12 |
alr | 3840719 | c.702A>G | synonymous_variant | 0.2 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.2 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.28 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.83 |
embC | 4239842 | c.-21C>A | upstream_gene_variant | 0.26 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.82 |
embC | 4240750 | c.888C>T | synonymous_variant | 0.81 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.78 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245321 | p.Met697Val | missense_variant | 0.79 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.8 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.78 |
aftB | 4267517 | c.1320A>G | synonymous_variant | 0.76 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.79 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.89 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.82 |
ethR | 4327450 | c.-99G>A | upstream_gene_variant | 0.8 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.85 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.9 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.71 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.22 |