Run ID: SRR6650391
Sample name:
Date: 15-08-2023 08:01:50
Number of reads: 1296455
Percentage reads mapped: 99.3
Strain: lineage1.1.3.1
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 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 1.0 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 1.0 |
lineage1.1.3.1 | Indo-Oceanic | NA | RD239 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6913 | p.Asn558Lys | missense_variant | 0.15 |
gyrA | 6922 | c.-380G>T | upstream_gene_variant | 0.17 |
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 |
fgd1 | 490751 | c.-32T>G | upstream_gene_variant | 0.18 |
fgd1 | 490759 | c.-24A>T | upstream_gene_variant | 0.27 |
fgd1 | 490771 | c.-12T>G | upstream_gene_variant | 0.23 |
fgd1 | 490784 | p.Val1Gly | missense_variant | 0.18 |
fgd1 | 490787 | p.Ala2Gly | missense_variant | 0.18 |
fgd1 | 491027 | p.Asn82Thr | missense_variant | 0.19 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576720 | p.Glu458Gly | missense_variant | 0.15 |
mshA | 576723 | p.Val459Gly | missense_variant | 0.17 |
ccsA | 620537 | p.Val216Gly | missense_variant | 0.16 |
ccsA | 620551 | p.Asp221His | missense_variant | 0.27 |
ccsA | 620748 | c.858T>G | synonymous_variant | 0.21 |
ccsA | 620756 | p.Asp289Gly | missense_variant | 0.17 |
ccsA | 620761 | p.Lys291Gln | missense_variant | 0.13 |
rpoB | 759611 | c.-196G>C | upstream_gene_variant | 0.22 |
rpoB | 759615 | c.-192A>C | upstream_gene_variant | 0.33 |
rpoB | 759618 | c.-189T>C | upstream_gene_variant | 0.17 |
rpoB | 759620 | c.-187A>C | upstream_gene_variant | 0.28 |
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 | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 765230 | p.Ala621Thr | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777572 | c.909C>T | synonymous_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801287 | p.Val160Gly | missense_variant | 0.21 |
fbiC | 1303016 | p.Val29Gly | missense_variant | 0.2 |
fbiC | 1304159 | p.Val410Gly | missense_variant | 0.21 |
fbiC | 1304166 | c.1236A>G | synonymous_variant | 0.19 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
atpE | 1461101 | c.57T>G | synonymous_variant | 0.22 |
atpE | 1461119 | c.75T>G | synonymous_variant | 0.24 |
atpE | 1461125 | c.81T>G | synonymous_variant | 0.18 |
atpE | 1461131 | c.87T>G | synonymous_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918066 | p.Ala43Pro | missense_variant | 0.17 |
ndh | 2103225 | c.-183A>C | upstream_gene_variant | 0.24 |
ndh | 2103235 | c.-193C>G | upstream_gene_variant | 0.16 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2169314 | p.Asn433Lys | missense_variant | 0.16 |
PPE35 | 2169317 | c.1296C>T | synonymous_variant | 0.15 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289380 | c.-139G>T | upstream_gene_variant | 0.15 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518147 | c.33C>T | synonymous_variant | 0.25 |
kasA | 2518151 | p.Ser13Arg | missense_variant | 0.27 |
eis | 2714549 | p.Met262Leu | missense_variant | 0.16 |
eis | 2714566 | p.Leu256Pro | missense_variant | 0.2 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726265 | p.Lys25Gln | missense_variant | 0.15 |
ahpC | 2726269 | p.Val26Gly | missense_variant | 0.19 |
ahpC | 2726279 | c.87G>A | synonymous_variant | 0.15 |
ahpC | 2726338 | p.Val49Gly | missense_variant | 0.35 |
ahpC | 2726341 | p.Val50Gly | missense_variant | 0.4 |
ahpC | 2726343 | p.Phe51Val | missense_variant | 0.15 |
ahpC | 2726350 | p.Trp53Leu | missense_variant | 0.42 |
ahpC | 2726360 | p.Asp56Glu | missense_variant | 0.15 |
ahpC | 2726366 | c.174G>C | synonymous_variant | 0.15 |
ribD | 2987316 | p.Ala160Pro | missense_variant | 0.14 |
ribD | 2987323 | p.Val162Gly | missense_variant | 0.23 |
ribD | 2987325 | p.Ile163Val | missense_variant | 0.19 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
thyA | 3074641 | c.-170C>T | upstream_gene_variant | 0.27 |
thyA | 3074645 | c.-174T>G | upstream_gene_variant | 0.27 |
thyA | 3074648 | c.-177T>G | upstream_gene_variant | 0.29 |
thyA | 3074652 | c.-181T>G | upstream_gene_variant | 0.14 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3449093 | p.Ala197Gly | missense_variant | 0.18 |
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 | 0.22 |
alr | 3841253 | c.168C>T | synonymous_variant | 1.0 |
alr | 3841277 | c.144C>T | synonymous_variant | 1.0 |
clpC1 | 4039435 | p.Phe424Val | missense_variant | 0.16 |
clpC1 | 4039471 | p.Ile412Val | missense_variant | 0.17 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243350 | p.Thr40Pro | missense_variant | 0.18 |
embA | 4243372 | p.Gln47Arg | missense_variant | 0.18 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4244641 | p.Val470Gly | missense_variant | 0.18 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4249314 | p.Phe934Ser | missense_variant | 0.18 |
embB | 4249323 | p.Ala937Glu | missense_variant | 0.25 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
ubiA | 4269502 | p.Val111Gly | missense_variant | 0.19 |
aftB | 4269504 | c.-668A>G | upstream_gene_variant | 0.24 |
ubiA | 4269511 | p.Val108Gly | missense_variant | 0.33 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326887 | p.Asp196Gly | missense_variant | 0.16 |
ethR | 4326898 | c.-651C>G | upstream_gene_variant | 0.15 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407780 | c.423G>A | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
whiB6 | 4338429 | c.-218_92del | frameshift_variant&start_lost | 1.0 |