Run ID: SRR20969464
Sample name:
Date: 03-04-2023 22:06:33
Number of reads: 10383786
Percentage reads mapped: 99.64
Strain: lineage4.5;lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.81 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.19 |
lineage4.5 | Euro-American | H;T | RD122 | 0.19 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.8 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.2 | rifampicin |
rpoC | 764363 | p.Gly332Arg | missense_variant | 0.23 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.15 | isoniazid |
pncA | 2288853 | c.386_388delATG | disruptive_inframe_deletion | 0.19 | pyrazinamide |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 0.16 | ethambutol |
gid | 4408100 | c.102delG | frameshift_variant | 0.18 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7892 | c.591G>A | synonymous_variant | 0.2 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.82 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.79 |
ccsA | 620029 | c.139C>T | synonymous_variant | 0.25 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.79 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.79 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.83 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.76 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.84 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.81 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1473294 | n.1449A>C | non_coding_transcript_exon_variant | 0.23 |
rpsA | 1833701 | p.Asp54Asn | missense_variant | 0.19 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.8 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.81 |
katG | 2155677 | c.435C>A | synonymous_variant | 0.19 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.82 |
PPE35 | 2170568 | p.Ile15Met | missense_variant | 0.21 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.77 |
fbiD | 3339480 | p.Gln121His | missense_variant | 0.19 |
Rv3083 | 3448508 | p.Asn2Ser | missense_variant | 0.82 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.8 |
rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 0.28 |
ddn | 3987001 | p.Gly53Asp | missense_variant | 0.14 |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 0.17 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.79 |
embB | 4247841 | p.Gly443Asp | missense_variant | 0.17 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.84 |
ethA | 4327875 | c.-402C>A | upstream_gene_variant | 0.16 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.82 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.77 |