Run ID: SRR6832857
Sample name:
Date: 04-04-2023 17:41:24
Number of reads: 1899099
Percentage reads mapped: 99.56
Strain: lineage4.2.1;lineage2.2.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.87 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.16 |
lineage4.2 | Euro-American | H;T;LAM | None | 0.14 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.88 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.86 |
lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 0.13 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
ahpC | 2726141 | c.-52C>T | upstream_gene_variant | 0.23 | isoniazid |
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 | 491247 | c.465C>T | synonymous_variant | 0.12 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.86 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.97 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.84 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.89 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.89 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.9 |
mmpR5 | 779251 | p.Asp88Asn | missense_variant | 0.11 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.82 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.93 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473937 | n.280C>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476222 | n.2565A>C | non_coding_transcript_exon_variant | 0.12 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.93 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.85 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.84 |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339665 | p.Pro183Leu | missense_variant | 0.79 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.75 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.89 |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.18 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.67 |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.38 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.91 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.79 |