Run ID: SRR3743370
Sample name:
Date: 04-04-2023 05:41:03
Number of reads: 892613
Percentage reads mapped: 99.44
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 | 0.98 |
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 |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.15 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289213 | p.Gln10Pro | missense_variant | 1.0 | pyrazinamide |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid |
thyA | 3073808 | p.Arg222Gly | missense_variant | 1.0 | para-aminosalicylic_acid |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | 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 |
fgd1 | 490877 | p.Met32Thr | missense_variant | 0.18 |
fgd1 | 490966 | p.Gly62Cys | missense_variant | 0.11 |
fgd1 | 490984 | p.Leu68Met | missense_variant | 0.12 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575180 | c.-168G>T | upstream_gene_variant | 0.1 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 760594 | p.Gly263Asp | missense_variant | 0.14 |
rpoB | 761268 | p.Ile488Val | missense_variant | 1.0 |
rpoC | 762485 | c.-885G>T | upstream_gene_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 765567 | c.2200delG | frameshift_variant | 0.12 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 1.0 |
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 | 778394 | c.-596A>G | upstream_gene_variant | 0.11 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
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 |
Rv1979c | 2223015 | c.150C>T | synonymous_variant | 0.11 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289668 | c.-427G>C | upstream_gene_variant | 0.13 |
eis | 2714750 | p.Val195Met | missense_variant | 0.11 |
folC | 2747479 | p.Glu40Asp | missense_variant | 0.15 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449348 | p.Asp282Val | missense_variant | 0.12 |
Rv3083 | 3449530 | p.Val343Phe | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475139 | p.Thr378Ser | missense_variant | 0.12 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3641810 | c.276G>C | synonymous_variant | 1.0 |
clpC1 | 4039601 | c.1104G>A | synonymous_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.17 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.17 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4326339 | p.Asn379Asp | 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 |
gid | 4408089 | c.114C>T | synonymous_variant | 0.13 |