Run ID: SRR1163360
Sample name:
Date: 02-04-2023 23:37:26
Number of reads: 1033026
Percentage reads mapped: 98.63
Strain: lineage4.1.2.1;lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.78 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.26 |
lineage4.1 | Euro-American | T;X;H | None | 0.25 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.78 |
lineage4.1.2 | Euro-American | T;H | None | 0.11 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.82 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.16 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.85 | rifampicin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.79 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.89 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.84 | isoniazid |
pncA | 2289248 | c.-7T>C | upstream_gene_variant | 0.68 | pyrazinamide |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 0.76 | ethambutol |
embB | 4247513 | p.Tyr334His | missense_variant | 0.83 | ethambutol |
embB | 4247618 | p.Val369Leu | missense_variant | 0.11 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9340 | p.Ser680Tyr | missense_variant | 0.15 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.28 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.8 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.36 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.85 |
ccsA | 620550 | c.660C>G | synonymous_variant | 0.17 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.7 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.21 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.94 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.76 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.87 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.83 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.75 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.88 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.93 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.89 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.88 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154397 | p.Thr572Met | missense_variant | 0.13 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.64 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.71 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.19 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.29 |
kasA | 2518745 | c.633delC | frameshift_variant | 0.13 |
folC | 2746575 | p.Met342Leu | missense_variant | 0.14 |
folC | 2747651 | c.-53C>G | upstream_gene_variant | 0.18 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087026 | p.Asp69Glu | missense_variant | 0.1 |
ald | 3087532 | p.Ala238Asp | missense_variant | 0.78 |
Rv3083 | 3449612 | p.Lys370Arg | missense_variant | 0.1 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612229 | c.888C>T | synonymous_variant | 0.56 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.75 |
embC | 4241018 | p.Leu386Val | missense_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.11 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.11 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.12 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.12 |
embB | 4248493 | p.Met660Ile | missense_variant | 0.26 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.8 |
aftB | 4269339 | c.-503C>T | upstream_gene_variant | 0.89 |
ethA | 4328085 | c.-612G>A | upstream_gene_variant | 0.15 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.77 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.75 |