Run ID: ERR4011933
Sample name:
Date: 01-04-2023 03:57:13
Number of reads: 2439711
Percentage reads mapped: 99.58
Strain: lineage4.6.3;lineage3.1.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.5 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.51 |
lineage4.6 | Euro-American | T;LAM | None | 0.48 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 0.47 |
lineage3.1.1 | East-African-Indian | CAS1-Kili | RD750 | 0.52 |
lineage4.6.3 | Euro-American | T;LAM | None | 0.48 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.43 | rifampicin |
rrs | 1472751 | n.906A>G | non_coding_transcript_exon_variant | 0.5 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.33 | isoniazid |
pncA | 2288887 | p.Trp119Arg | missense_variant | 0.58 | pyrazinamide |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.53 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8049 | p.Ser250Ala | missense_variant | 0.58 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.45 |
ccsA | 620072 | p.Pro61Leu | missense_variant | 0.56 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.57 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.53 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.54 |
rpoC | 765462 | p.Asn698Ser | missense_variant | 0.55 |
rpoC | 765519 | p.Lys717Thr | missense_variant | 0.52 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.5 |
mmpL5 | 776987 | c.1493delC | frameshift_variant | 0.43 |
mmpS5 | 778673 | p.Pro78Leu | missense_variant | 0.54 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.57 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.44 |
PPE35 | 2170461 | p.Gly51Glu | missense_variant | 0.48 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.58 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.54 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.52 |
pepQ | 2860371 | c.48C>T | synonymous_variant | 0.59 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.47 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.97 |
fbiB | 3640824 | c.-711C>A | upstream_gene_variant | 0.56 |
embC | 4240172 | p.Val104Met | missense_variant | 0.53 |
embC | 4241562 | p.Arg567His | missense_variant | 0.59 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.48 |
embC | 4242185 | p.Asp775Asn | missense_variant | 0.4 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.99 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.22 |
aftB | 4268573 | p.Met88Ile | missense_variant | 0.51 |
ubiA | 4269162 | p.Leu224Phe | missense_variant | 0.54 |
whiB6 | 4338268 | p.Gly85Ala | missense_variant | 0.46 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338635 | c.-114A>G | upstream_gene_variant | 0.49 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.56 |
gid | 4407934 | p.Leu90Arg | missense_variant | 0.48 |