Run ID: ERR11043505
Sample name:
Date: 31-03-2023 11:35:41
Number of reads: 5316411
Percentage reads mapped: 99.47
Strain: lineage5;lineage4.2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.86 |
lineage5 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 0.12 |
lineage4.2 | Euro-American | H;T;LAM | None | 0.85 |
lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.85 |
lineage4.2.2.1 | Euro-American | LAM7-TUR | None | 0.86 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761095 | p.Leu430Pro | missense_variant | 0.11 | rifampicin |
rpoB | 761110 | p.Asp435Gly | missense_variant | 0.12 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.81 | rifampicin |
rrs | 1473183 | n.1338A>C | non_coding_transcript_exon_variant | 0.11 | aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.87 | isoniazid |
pncA | 2289028 | p.Cys72Arg | missense_variant | 0.2 | pyrazinamide |
ahpC | 2726139 | c.-54C>T | upstream_gene_variant | 0.15 | isoniazid |
embB | 4248002 | p.Gln497Lys | missense_variant | 0.86 | ethambutol |
gid | 4407944 | c.258_259insG | frameshift_variant | 0.82 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.16 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.12 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9566 | c.2265C>T | synonymous_variant | 0.15 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.19 |
mshA | 576077 | c.730C>T | synonymous_variant | 0.88 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.24 |
rpoB | 760677 | p.Glu291Lys | missense_variant | 0.17 |
rpoB | 760994 | c.1188G>A | synonymous_variant | 0.15 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.11 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.16 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101921 | c.1122G>A | synonymous_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.15 |
eis | 2714510 | c.823T>C | synonymous_variant | 0.15 |
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.84 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.87 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339000 | c.-117_-116delCA | upstream_gene_variant | 0.13 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
alr | 3840932 | c.489C>T | synonymous_variant | 0.13 |
ddn | 3986987 | c.144G>T | synonymous_variant | 0.12 |
ddn | 3987180 | p.Asp113Asn | missense_variant | 0.12 |
clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 0.15 |
embC | 4239843 | c.-20A>C | upstream_gene_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244220 | c.988C>T | synonymous_variant | 0.13 |
embA | 4245147 | p.Pro639Ser | missense_variant | 0.16 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.22 |
embB | 4247465 | p.Asn318Asp | missense_variant | 0.18 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.17 |
embB | 4248616 | c.2103G>T | synonymous_variant | 0.15 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.18 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.16 |
ethA | 4326533 | p.Thr314Ile | missense_variant | 0.88 |
ethA | 4326977 | p.His166Pro | missense_variant | 0.11 |
ethA | 4327103 | p.Gly124Asp | missense_variant | 0.18 |
ethA | 4328322 | c.-849G>T | upstream_gene_variant | 0.16 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.11 |
gid | 4407947 | p.Leu86Phe | missense_variant | 0.19 |