Run ID: SRR6650385
Sample name:
Date: 15-08-2023 07:38:49
Number of reads: 529026
Percentage reads mapped: 99.33
Strain: lineage1.2.2.2
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | ||
Ethambutol | R | embB p.Asp354Ala (0.22) |
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 | 1.0 |
lineage1.2.2.2 | Indo-Oceanic | NA | RD239 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
embB | 4247574 | p.Asp354Ala | missense_variant | 0.22 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6182 | p.Thr315Ala | missense_variant | 1.0 |
gyrA | 7268 | c.-34C>T | upstream_gene_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 | 8674 | p.Ile458Thr | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9585 | p.Leu762Val | missense_variant | 0.33 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576723 | p.Val459Gly | missense_variant | 0.36 |
ccsA | 620551 | p.Asp221His | missense_variant | 0.22 |
ccsA | 620748 | c.858T>G | synonymous_variant | 0.42 |
ccsA | 620752 | p.Arg288Gly | missense_variant | 0.5 |
ccsA | 620756 | p.Asp289Gly | missense_variant | 0.58 |
ccsA | 620761 | p.Lys291Gln | missense_variant | 0.17 |
ccsA | 620765 | p.Ala292Gly | missense_variant | 0.18 |
ccsA | 620770 | p.Trp294Arg | missense_variant | 0.27 |
ccsA | 620773 | p.Ile295Val | missense_variant | 0.64 |
ccsA | 620779 | p.Val297Phe | missense_variant | 0.18 |
ccsA | 620788 | p.Phe300Leu | missense_variant | 0.18 |
ccsA | 620801 | p.Val304Gly | missense_variant | 0.18 |
rpoB | 760703 | c.897C>T | synonymous_variant | 1.0 |
rpoB | 761725 | p.Glu640Gly | missense_variant | 1.0 |
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 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 778270 | p.Ser71Ala | missense_variant | 0.25 |
mmpL5 | 778282 | p.Asp67His | missense_variant | 0.18 |
mmpR5 | 779348 | p.Val120Gly | missense_variant | 0.25 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801287 | p.Val160Gly | missense_variant | 0.6 |
fbiC | 1303016 | p.Val29Gly | missense_variant | 0.33 |
Rv1258c | 1406452 | p.Thr297Pro | missense_variant | 0.17 |
Rv1258c | 1407081 | p.Ala87Gly | missense_variant | 0.33 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1476219 | n.2562T>G | non_coding_transcript_exon_variant | 0.17 |
fabG1 | 1674076 | p.Thr213Pro | missense_variant | 0.18 |
rpsA | 1834666 | c.1125G>A | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918010 | p.Ala24Gly | missense_variant | 0.22 |
tlyA | 1918029 | c.90C>A | synonymous_variant | 0.22 |
tlyA | 1918055 | p.Ala39Gly | missense_variant | 0.25 |
tlyA | 1918059 | c.120C>A | synonymous_variant | 0.38 |
ndh | 2103225 | c.-183A>C | upstream_gene_variant | 0.88 |
ndh | 2103227 | c.-185T>C | upstream_gene_variant | 0.5 |
ndh | 2103229 | c.-187C>A | upstream_gene_variant | 0.25 |
ndh | 2103235 | c.-193C>G | upstream_gene_variant | 0.86 |
ndh | 2103239 | c.-197T>G | upstream_gene_variant | 0.38 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167660 | p.Thr985Pro | missense_variant | 0.33 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 1.0 |
PPE35 | 2168885 | c.1728A>C | synonymous_variant | 1.0 |
PPE35 | 2169293 | c.1320T>G | synonymous_variant | 0.2 |
PPE35 | 2170056 | p.Val186Gly | missense_variant | 0.18 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
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 | 2714569 | p.Ala255Gly | missense_variant | 0.2 |
eis | 2714670 | p.Asp221Glu | missense_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ribD | 2987323 | p.Val162Gly | missense_variant | 0.25 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087909 | p.Thr364Pro | missense_variant | 0.38 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3448813 | p.Val104Phe | missense_variant | 0.25 |
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 |
whiB7 | 3568417 | p.Lys88Arg | missense_variant | 0.15 |
whiB7 | 3568419 | c.261C>A | synonymous_variant | 0.15 |
Rv3236c | 3612776 | p.Asp114Gly | missense_variant | 0.22 |
Rv3236c | 3612780 | p.Leu113Val | missense_variant | 0.22 |
Rv3236c | 3612784 | p.Leu111Phe | missense_variant | 0.22 |
Rv3236c | 3612789 | p.Leu110Val | missense_variant | 0.22 |
Rv3236c | 3612797 | p.Ala107Gly | missense_variant | 0.22 |
Rv3236c | 3612800 | p.Val106Gly | missense_variant | 0.22 |
Rv3236c | 3612835 | c.282T>G | synonymous_variant | 0.5 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4239973 | c.111T>G | synonymous_variant | 0.17 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4242220 | c.2358A>C | synonymous_variant | 0.25 |
embA | 4242406 | c.-827A>C | upstream_gene_variant | 0.22 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243350 | p.Thr40Pro | missense_variant | 0.18 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247577 | p.Leu355Arg | missense_variant | 0.22 |
embB | 4247590 | c.1077A>G | synonymous_variant | 0.17 |
embB | 4247599 | p.Trp362Cys | missense_variant | 0.2 |
embB | 4247607 | p.Leu365Arg | missense_variant | 0.18 |
embB | 4247614 | c.1101T>G | synonymous_variant | 0.2 |
embB | 4247616 | p.Glu368Gly | missense_variant | 0.2 |
embB | 4247619 | p.Val369Gly | missense_variant | 0.2 |
embB | 4247623 | c.1110G>C | synonymous_variant | 0.3 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4249403 | p.Thr964Pro | missense_variant | 0.5 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269504 | c.-668A>G | upstream_gene_variant | 0.2 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326148 | c.1326G>T | synonymous_variant | 1.0 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 |
ethA | 4326887 | p.Asp196Gly | missense_variant | 0.33 |
ethR | 4327639 | p.Ala31Pro | missense_variant | 0.2 |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |