Run ID: SRR6650368
Sample name:
Date: 15-08-2023 08:00:40
Number of reads: 560874
Percentage reads mapped: 99.33
Strain: lineage1.2.2.2
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | ||
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 0.98 |
lineage1.2.2.2 | Indo-Oceanic | NA | RD239 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 |
gyrB | 5530 | c.291C>T | synonymous_variant | 1.0 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9701 | c.2400T>G | synonymous_variant | 0.15 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576723 | p.Val459Gly | missense_variant | 0.33 |
ccsA | 620586 | c.696C>T | synonymous_variant | 1.0 |
ccsA | 620748 | c.858T>G | synonymous_variant | 0.36 |
ccsA | 620752 | p.Arg288Gly | missense_variant | 0.31 |
ccsA | 620756 | p.Asp289Gly | missense_variant | 0.33 |
ccsA | 620773 | p.Ile295Val | missense_variant | 0.25 |
rpoB | 759620 | c.-187A>C | upstream_gene_variant | 0.5 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 765889 | c.2520C>T | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777155 | c.1326G>C | synonymous_variant | 1.0 |
mmpL5 | 777427 | p.Thr352Pro | missense_variant | 0.2 |
mmpR5 | 779348 | p.Val120Gly | missense_variant | 0.39 |
mmpR5 | 779356 | p.Arg123Gly | missense_variant | 0.17 |
mmpR5 | 779363 | p.Leu125Arg | missense_variant | 0.13 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302948 | c.18T>G | synonymous_variant | 1.0 |
fbiC | 1304166 | c.1236A>G | synonymous_variant | 0.25 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
atpE | 1461086 | c.42A>G | synonymous_variant | 0.5 |
atpE | 1461125 | c.81T>G | synonymous_variant | 0.4 |
atpE | 1461131 | c.87T>G | synonymous_variant | 0.33 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1833549 | p.Ser3Asn | missense_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918059 | c.120C>A | synonymous_variant | 0.25 |
ndh | 2103225 | c.-183A>C | upstream_gene_variant | 0.56 |
ndh | 2103227 | c.-185T>C | upstream_gene_variant | 0.38 |
ndh | 2103235 | c.-193C>G | upstream_gene_variant | 0.71 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167660 | p.Thr985Pro | missense_variant | 0.25 |
PPE35 | 2167859 | c.2754T>G | synonymous_variant | 0.2 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.25 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289511 | c.-270T>G | upstream_gene_variant | 0.29 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518147 | c.33C>T | synonymous_variant | 0.27 |
kasA | 2518151 | p.Ser13Arg | missense_variant | 0.2 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726269 | p.Val26Gly | missense_variant | 0.29 |
pepQ | 2859414 | c.1005T>G | synonymous_variant | 0.24 |
pepQ | 2859454 | p.Val322Gly | missense_variant | 0.29 |
ribD | 2987316 | p.Ala160Pro | missense_variant | 0.22 |
Rv2752c | 3064889 | p.Lys435Glu | missense_variant | 1.0 |
Rv2752c | 3066103 | p.Asn30Ser | missense_variant | 0.92 |
thyA | 3074641 | c.-170C>T | upstream_gene_variant | 0.29 |
thyA | 3074645 | c.-174T>G | upstream_gene_variant | 0.29 |
thyA | 3074648 | c.-177T>G | upstream_gene_variant | 0.25 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339273 | c.156T>G | synonymous_variant | 0.2 |
fbiD | 3339279 | c.162T>G | synonymous_variant | 0.17 |
fbiD | 3339593 | p.His159Pro | missense_variant | 0.19 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
Rv3236c | 3612835 | c.282T>G | synonymous_variant | 0.2 |
fbiB | 3642754 | p.Leu407Arg | missense_variant | 0.22 |
alr | 3841515 | c.-95C>A | upstream_gene_variant | 0.14 |
alr | 3841528 | c.-108A>C | upstream_gene_variant | 0.18 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 1.0 |
clpC1 | 4038163 | p.Arg848Gly | missense_variant | 0.18 |
clpC1 | 4038874 | p.Thr611Pro | missense_variant | 0.18 |
clpC1 | 4039484 | c.1221T>G | synonymous_variant | 0.27 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4240006 | c.144A>C | synonymous_variant | 0.18 |
embC | 4240039 | p.Leu59Phe | missense_variant | 0.15 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.88 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241433 | p.Met524Arg | missense_variant | 0.33 |
embC | 4242414 | p.Leu851Arg | missense_variant | 0.31 |
embC | 4242422 | p.Trp854Gly | missense_variant | 0.21 |
embC | 4242425 | p.Arg855Gly | missense_variant | 0.14 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4242952 | c.-281T>G | upstream_gene_variant | 0.18 |
embA | 4243398 | p.Thr56Pro | missense_variant | 0.2 |
embA | 4244905 | p.Val558Gly | missense_variant | 0.25 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247623 | c.1110G>C | synonymous_variant | 0.29 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4249190 | p.Thr893Pro | missense_variant | 0.2 |
embB | 4249305 | p.Asn931Thr | missense_variant | 0.25 |
embB | 4249323 | p.Ala937Glu | missense_variant | 0.29 |
aftB | 4268758 | p.Ile27Val | missense_variant | 0.5 |
aftB | 4268774 | p.Ser21Gly | missense_variant | 0.4 |
aftB | 4268786 | c.51C>T | synonymous_variant | 0.75 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ubiA | 4269859 | c.-26A>C | upstream_gene_variant | 0.29 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338635 | c.-114A>C | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |