Run ID: ERR10680134
Sample name:
Date: 31-03-2023 10:38:14
Number of reads: 3853475
Percentage reads mapped: 99.31
Strain: lineage6.2.2
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage6 | West-Africa 2 | AFRI_1 | RD702 | 1.0 |
lineage6.2 | West-Africa 2 | AFRI_1 | RD702 | 1.0 |
lineage6.2.2 | West-Africa 2 | AFRI_1 | RD702 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761093 | p.Gln429His | missense_variant | 0.92 | rifampicin |
rpoB | 761095 | p.Leu430Pro | missense_variant | 0.92 | rifampicin |
rpoB | 761141 | p.His445Gln | missense_variant | 0.88 | rifampicin |
katG | 2155709 | c.392_402delCGCTTAACAGC | frameshift_variant | 0.86 | isoniazid |
pncA | 2289202 | p.Cys14Arg | missense_variant | 0.82 | pyrazinamide |
ahpC | 2726112 | c.-81C>T | upstream_gene_variant | 0.86 | isoniazid |
embB | 4249518 | p.His1002Arg | missense_variant | 0.9 | ethambutol |
embB | 4249583 | p.Asp1024Asn | missense_variant | 0.28 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5072 | c.-168G>T | upstream_gene_variant | 1.0 |
gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8493 | p.Leu398Phe | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.99 |
fgd1 | 491668 | p.Lys296Glu | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.2 |
rpoB | 760939 | p.Leu378Arg | missense_variant | 0.12 |
rpoB | 760969 | p.Ser388Leu | missense_variant | 1.0 |
rpoB | 761723 | p.Glu639Asp | missense_variant | 1.0 |
rpoB | 762041 | c.2235C>T | synonymous_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777407 | p.Ile358Met | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 |
Rv1258c | 1406685 | p.Val219Ala | missense_variant | 1.0 |
embR | 1416633 | p.Leu239Val | missense_variant | 1.0 |
atpE | 1461251 | c.207G>T | synonymous_variant | 0.99 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1674434 | p.Val78Ala | missense_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155503 | c.609C>T | synonymous_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
ahpC | 2726142 | c.-51G>A | upstream_gene_variant | 0.14 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.17 |
ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.53 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
whiB7 | 3568605 | c.75C>T | synonymous_variant | 1.0 |
Rv3236c | 3612800 | p.Val106Ala | missense_variant | 1.0 |
alr | 3840559 | p.Arg288Ser | missense_variant | 1.0 |
alr | 3840618 | p.Asp268Gly | missense_variant | 1.0 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.18 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241843 | p.Leu661Ile | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243225 | c.-8C>G | upstream_gene_variant | 0.11 |
embA | 4243541 | c.309C>T | synonymous_variant | 1.0 |
embA | 4244220 | c.988C>T | synonymous_variant | 1.0 |
embA | 4244379 | p.Pro383Ser | missense_variant | 1.0 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.5 |
embB | 4246864 | c.351C>T | synonymous_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
aftB | 4269351 | c.-515C>T | upstream_gene_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269522 | c.-686C>T | upstream_gene_variant | 0.99 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326465 | p.Ile337Val | missense_variant | 1.0 |
ethR | 4326601 | c.-948C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |