Run ID: SRR6650404
Sample name:
Date: 15-08-2023 08:03:27
Number of reads: 1233022
Percentage reads mapped: 99.59
Strain: lineage2.2.1
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 |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.95 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.97 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.97 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6645 | p.Ser469Asn | missense_variant | 0.19 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491008 | p.Thr76Pro | missense_variant | 0.31 |
fgd1 | 491014 | p.Thr78Pro | missense_variant | 0.31 |
fgd1 | 491027 | p.Asn82Thr | missense_variant | 0.27 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576715 | c.1368C>G | synonymous_variant | 0.27 |
mshA | 576720 | p.Glu458Gly | missense_variant | 0.22 |
mshA | 576723 | p.Val459Gly | missense_variant | 0.4 |
mshA | 576744 | p.Val466Gly | missense_variant | 0.2 |
ccsA | 619707 | c.-184T>G | upstream_gene_variant | 0.2 |
ccsA | 619831 | c.-60T>G | upstream_gene_variant | 0.19 |
ccsA | 619835 | c.-56G>T | upstream_gene_variant | 0.22 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 759806 | c.-1C>T | upstream_gene_variant | 0.14 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 766920 | p.Ala1184Gly | missense_variant | 0.14 |
mmpL5 | 775603 | p.Thr960Pro | missense_variant | 0.29 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpR5 | 779336 | p.Asp116Ala | missense_variant | 0.3 |
mmpR5 | 779346 | p.Asp119Glu | missense_variant | 0.3 |
mmpR5 | 779348 | p.Val120Gly | missense_variant | 0.32 |
mmpR5 | 779354 | p.Leu122Arg | missense_variant | 0.19 |
mmpR5 | 779356 | p.Arg123Gly | missense_variant | 0.33 |
mmpR5 | 779363 | p.Leu125Arg | missense_variant | 0.35 |
mmpR5 | 779371 | p.Ala128Pro | missense_variant | 0.42 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.87 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801287 | p.Val160Gly | missense_variant | 0.29 |
rplC | 801291 | c.483C>T | synonymous_variant | 0.17 |
rplC | 801316 | p.Met170Val | missense_variant | 0.2 |
fbiC | 1303016 | p.Val29Gly | missense_variant | 0.25 |
Rv1258c | 1406452 | p.Thr297Pro | missense_variant | 0.25 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473916 | n.259C>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1473923 | n.266C>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1473932 | n.275C>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1473959 | n.302T>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474489 | n.832T>G | non_coding_transcript_exon_variant | 0.5 |
rrl | 1474500 | n.843T>G | non_coding_transcript_exon_variant | 0.4 |
fabG1 | 1674076 | p.Thr213Pro | missense_variant | 0.2 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.95 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918005 | c.66G>A | synonymous_variant | 0.14 |
tlyA | 1918013 | p.Glu25Gly | missense_variant | 0.19 |
tlyA | 1918052 | p.Pro38Arg | missense_variant | 0.3 |
tlyA | 1918059 | c.120C>A | synonymous_variant | 0.2 |
tlyA | 1918066 | p.Ala43Pro | missense_variant | 0.31 |
tlyA | 1918072 | p.Ala45Pro | missense_variant | 0.15 |
ndh | 2103222 | c.-180A>C | upstream_gene_variant | 0.17 |
ndh | 2103225 | c.-183A>C | upstream_gene_variant | 0.35 |
ndh | 2103227 | c.-185T>C | upstream_gene_variant | 0.3 |
ndh | 2103235 | c.-193C>G | upstream_gene_variant | 0.39 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167845 | p.Ser923Asn | missense_variant | 0.15 |
PPE35 | 2167859 | c.2754T>G | synonymous_variant | 0.31 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169854 | c.759T>G | synonymous_variant | 0.21 |
PPE35 | 2170045 | p.Thr190Pro | missense_variant | 0.18 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289386 | c.-145A>C | upstream_gene_variant | 0.19 |
pncA | 2289509 | c.-268A>G | upstream_gene_variant | 0.2 |
pncA | 2289511 | c.-270T>G | upstream_gene_variant | 0.21 |
pncA | 2289554 | c.-313G>T | upstream_gene_variant | 0.18 |
kasA | 2518147 | c.33C>T | synonymous_variant | 0.33 |
kasA | 2518151 | p.Ser13Arg | missense_variant | 0.41 |
kasA | 2518605 | p.Val164Gly | missense_variant | 0.32 |
eis | 2715560 | c.-228T>G | upstream_gene_variant | 0.24 |
ahpC | 2726265 | p.Lys25Gln | missense_variant | 0.21 |
ahpC | 2726269 | p.Val26Gly | missense_variant | 0.46 |
ahpC | 2726277 | p.Lys29Gln | missense_variant | 0.15 |
ahpC | 2726286 | p.Gly32Arg | missense_variant | 0.5 |
ahpC | 2726290 | p.Asp33Gly | missense_variant | 0.36 |
folC | 2746745 | p.Val285Gly | missense_variant | 0.27 |
pepQ | 2859377 | p.Thr348Ala | missense_variant | 0.18 |
pepQ | 2859414 | c.1005T>G | synonymous_variant | 0.24 |
pepQ | 2859425 | p.Gly332Arg | missense_variant | 0.19 |
pepQ | 2859438 | c.981T>G | synonymous_variant | 0.25 |
pepQ | 2859454 | p.Val322Gly | missense_variant | 0.23 |
thyA | 3073829 | p.Gln215Lys | missense_variant | 0.21 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339174 | p.Leu19Phe | missense_variant | 0.18 |
fbiD | 3339273 | c.156T>G | synonymous_variant | 0.31 |
fbiD | 3339281 | p.Ser55Leu | missense_variant | 0.18 |
fbiD | 3339310 | p.Asp65His | missense_variant | 0.16 |
Rv3083 | 3448484 | c.-20T>G | upstream_gene_variant | 0.18 |
Rv3083 | 3448765 | p.Thr88Pro | missense_variant | 0.23 |
Rv3083 | 3449107 | p.Gly202Arg | missense_variant | 0.18 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3611974 | c.1143A>C | synonymous_variant | 0.22 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
Rv3236c | 3612835 | c.282T>G | synonymous_variant | 0.3 |
fbiB | 3642744 | p.Ala404Ser | missense_variant | 0.5 |
rpoA | 3878238 | p.Asp90Glu | missense_variant | 0.3 |
ddn | 3986919 | p.Thr26Pro | missense_variant | 0.2 |
clpC1 | 4038163 | p.Arg848Gly | missense_variant | 0.24 |
clpC1 | 4039468 | p.Arg413Cys | missense_variant | 0.22 |
clpC1 | 4039471 | p.Ile412Val | missense_variant | 0.29 |
panD | 4044471 | c.-190T>G | upstream_gene_variant | 0.18 |
embC | 4239973 | c.111T>G | synonymous_variant | 0.29 |
embC | 4240006 | c.144A>C | synonymous_variant | 0.15 |
embC | 4242220 | c.2358A>C | synonymous_variant | 0.29 |
embC | 4242223 | c.2361C>A | synonymous_variant | 0.21 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242822 | p.Val987Gly | missense_variant | 0.24 |
embC | 4242996 | p.Val1045Gly | missense_variant | 0.25 |
embA | 4243350 | p.Thr40Pro | missense_variant | 0.32 |
embA | 4243372 | p.Gln47Arg | missense_variant | 0.16 |
embA | 4243380 | p.Thr50Pro | missense_variant | 0.16 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4247614 | c.1101T>G | synonymous_variant | 0.15 |
embB | 4247616 | p.Glu368Gly | missense_variant | 0.15 |
embB | 4247623 | c.1110G>C | synonymous_variant | 0.21 |
embB | 4247657 | p.Pro382Thr | missense_variant | 0.15 |
embB | 4249330 | p.Met939Ile | missense_variant | 0.18 |
embB | 4249757 | p.Thr1082Ala | missense_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.96 |
aftB | 4268799 | p.Val13Gly | missense_variant | 0.25 |
ubiA | 4269853 | c.-20C>G | upstream_gene_variant | 0.19 |
ubiA | 4269864 | c.-31C>G | upstream_gene_variant | 0.21 |
ethR | 4327813 | p.Thr89Pro | missense_variant | 0.17 |
whiB6 | 4338376 | p.Ala49Asp | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |