Run ID: ERR2516338
Sample name:
Date: 31-03-2023 21:28:11
Number of reads: 1463116
Percentage reads mapped: 99.29
Strain: lineage6.3.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage6 | West-Africa 2 | AFRI_1 | RD702 | 0.98 |
lineage6.3 | West-Africa 2 | AFRI_1 | RD702 | 1.0 |
lineage6.3.1 | West-Africa 2 | AFRI_1 | RD702 | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288817 | p.Thr142Lys | missense_variant | 1.0 | pyrazinamide |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.98 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490887 | c.105G>T | synonymous_variant | 0.36 |
fgd1 | 491668 | p.Lys296Glu | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575441 | p.Gly32Trp | missense_variant | 0.33 |
mshA | 575725 | c.378C>A | synonymous_variant | 0.17 |
rpoB | 760969 | p.Ser388Leu | missense_variant | 1.0 |
rpoB | 761193 | p.Gly463Trp | missense_variant | 0.24 |
rpoB | 761723 | p.Glu639Asp | missense_variant | 1.0 |
rpoB | 762184 | p.Gly793Val | missense_variant | 0.24 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775841 | c.2640G>A | synonymous_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776579 | c.1902G>T | synonymous_variant | 0.22 |
mmpL5 | 777274 | p.Val403Ile | missense_variant | 0.23 |
mmpL5 | 777338 | p.Lys381Asn | missense_variant | 0.17 |
mmpL5 | 777986 | c.495C>A | synonymous_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 0.97 |
atpE | 1461251 | c.207G>T | synonymous_variant | 1.0 |
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 |
ndh | 2102694 | p.Val117Ile | missense_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 |
PPE35 | 2169715 | p.Gly300Ser | missense_variant | 1.0 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2222852 | p.Ala105Thr | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
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 |
Rv3083 | 3448315 | c.-189C>A | upstream_gene_variant | 0.25 |
Rv3083 | 3449375 | p.Leu291Pro | missense_variant | 0.11 |
Rv3083 | 3449781 | c.1278G>A | synonymous_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474161 | p.Gly52Val | missense_variant | 0.2 |
fprA | 3475132 | p.Gln376Lys | missense_variant | 0.18 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fbiA | 3641071 | p.Arg177Ser | missense_variant | 0.2 |
fbiB | 3642860 | c.1326C>A | synonymous_variant | 0.2 |
fbiB | 3642873 | p.Leu447Met | missense_variant | 0.22 |
rpoA | 3877696 | p.Thr271Ile | missense_variant | 1.0 |
rpoA | 3878572 | c.-65G>T | upstream_gene_variant | 0.22 |
rpoA | 3878573 | c.-66G>T | upstream_gene_variant | 0.25 |
clpC1 | 4040173 | p.Leu178Ile | missense_variant | 0.2 |
panD | 4044176 | p.Ala36Thr | missense_variant | 0.2 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241843 | p.Leu661Ile | missense_variant | 1.0 |
embC | 4242193 | c.2331G>T | synonymous_variant | 0.23 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244220 | c.988C>T | synonymous_variant | 1.0 |
embA | 4244379 | p.Pro383Ser | missense_variant | 1.0 |
embB | 4246526 | p.Ala5Thr | missense_variant | 1.0 |
embB | 4246635 | p.Ser41* | stop_gained | 0.27 |
embB | 4246648 | c.135G>A | synonymous_variant | 0.2 |
embB | 4246864 | c.351C>T | synonymous_variant | 0.97 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248626 | p.Ala705Thr | missense_variant | 1.0 |
embB | 4249733 | p.Pro1074Thr | missense_variant | 0.18 |
aftB | 4268477 | c.360C>T | synonymous_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 | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326465 | p.Ile337Val | missense_variant | 1.0 |
ethA | 4327034 | p.Tyr147Cys | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407695 | p.Glu170Lys | missense_variant | 1.0 |