Run ID: SRR6256971
Sample name:
Date: 04-04-2023 13:21:15
Number of reads: 778584
Percentage reads mapped: 100.0
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288782 | p.Arg154Gly | missense_variant | 1.0 | pyrazinamide |
folC | 2747471 | p.Ile43Thr | missense_variant | 1.0 | para-aminosalicylic_acid |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4326341 | p.Pro378Leu | missense_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8116 | p.Thr272Ile | missense_variant | 0.1 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576780 | p.Val478Ala | missense_variant | 0.13 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 761260 | p.Gly485Ala | missense_variant | 0.2 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 766825 | p.Lys1152Asn | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776057 | c.2424G>T | synonymous_variant | 0.11 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 776665 | p.Thr606Pro | missense_variant | 0.12 |
mmpL5 | 777539 | c.942T>C | synonymous_variant | 0.11 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304900 | p.Arg657His | missense_variant | 0.1 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
embR | 1416579 | p.Gln257* | stop_gained | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1674930 | p.Cys243* | stop_gained | 0.29 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170398 | p.Tyr72Cys | missense_variant | 0.29 |
PPE35 | 2170465 | p.Ala50Thr | missense_variant | 0.2 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288842 | p.Ala134Thr | missense_variant | 1.0 |
pncA | 2289820 | c.-579T>G | upstream_gene_variant | 0.18 |
eis | 2714995 | p.Tyr113Cys | missense_variant | 0.12 |
ahpC | 2726341 | p.Val50Gly | missense_variant | 0.25 |
folC | 2746995 | p.Val202Phe | missense_variant | 0.12 |
folC | 2747062 | c.537A>G | synonymous_variant | 0.1 |
folC | 2747185 | c.414G>C | synonymous_variant | 0.11 |
pepQ | 2859380 | p.Gly347Arg | missense_variant | 0.11 |
Rv2752c | 3065520 | c.672G>T | synonymous_variant | 0.12 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087145 | p.Asp109Gly | missense_variant | 0.11 |
ald | 3087678 | p.Thr287Ser | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474437 | p.Asp144Gly | missense_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3640851 | c.-684G>A | upstream_gene_variant | 0.12 |
ddn | 3986739 | c.-105T>C | upstream_gene_variant | 0.12 |
clpC1 | 4039300 | p.Arg469Ser | missense_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243222 | c.-11C>T | upstream_gene_variant | 1.0 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4244537 | c.1305T>G | synonymous_variant | 0.1 |
embB | 4249635 | p.Asp1041Val | missense_variant | 0.12 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4327827 | c.-354A>G | upstream_gene_variant | 0.12 |
whiB6 | 4338317 | p.Ser69Thr | missense_variant | 0.15 |
whiB6 | 4338371 | p.Thr51Pro | 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 |