Run ID: SRR10430396
Sample name:
Date: 02-04-2023 17:42:53
Number of reads: 3137985
Percentage reads mapped: 99.54
Strain: lineage4.3.2.1;lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.79 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.17 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.18 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.84 |
lineage4.3.2 | Euro-American (LAM) | LAM3 | None | 0.17 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.84 |
lineage4.3.2.1 | Euro-American (LAM) | LAM3 | RD761 | 0.14 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.81 | streptomycin |
rpsL | 781821 | p.Lys88Gln | missense_variant | 0.16 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288818 | p.Thr142Ala | missense_variant | 0.8 | pyrazinamide |
pncA | 2288955 | p.Lys96Thr | missense_variant | 0.14 | pyrazinamide |
embB | 4246734 | p.Leu74Arg | missense_variant | 0.87 | ethambutol |
embB | 4247431 | p.Met306Ile | missense_variant | 0.12 | ethambutol |
embB | 4247496 | p.Asp328Gly | missense_variant | 0.85 | ethambutol |
ethA | 4326426 | c.1047delT | frameshift_variant | 0.99 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5520 | p.Pro94Leu | missense_variant | 0.23 |
gyrA | 7222 | c.-80C>T | upstream_gene_variant | 0.2 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8164 | p.Ala288Asp | missense_variant | 0.14 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.82 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.78 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.39 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.77 |
rpoB | 761004 | p.Thr400Gly | missense_variant | 0.17 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.81 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.18 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.87 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.78 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.79 |
mmpR5 | 779120 | p.Leu44Pro | missense_variant | 0.22 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.83 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.85 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 0.14 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.81 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.86 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.78 |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.27 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290107 | c.-866T>A | upstream_gene_variant | 0.2 |
Rv2752c | 3064974 | p.Asn406Lys | missense_variant | 0.87 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.39 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.79 |
fbiA | 3640407 | c.-136G>A | upstream_gene_variant | 0.17 |
rpoA | 3878613 | c.-106A>C | upstream_gene_variant | 0.3 |
rpoA | 3878637 | c.-130G>C | upstream_gene_variant | 0.19 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.29 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.19 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.84 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.22 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.82 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.77 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.78 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.24 |