Run ID: SRR3105745
Sample name:
Date: 04-04-2023 05:08:00
Number of reads: 4804956
Percentage reads mapped: 97.74
Strain: lineage4;lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.92 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.08 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.8 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Trp | missense_variant | 0.93 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.11 | isoniazid |
embB | 4247730 | p.Gly406Asp | missense_variant | 0.96 | ethambutol |
gid | 4408100 | c.102delG | frameshift_variant | 0.91 | streptomycin |
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 | 491742 | c.960T>C | synonymous_variant | 0.92 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.9 |
rpoB | 760719 | p.Val305Ile | missense_variant | 0.63 |
rpoB | 761850 | p.Pro682Ala | missense_variant | 0.11 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.9 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.84 |
rpoC | 767314 | p.Tyr1315* | stop_gained | 0.38 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.88 |
mmpL5 | 777320 | c.1161C>G | synonymous_variant | 0.13 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1833742 | p.Glu67Asp | missense_variant | 0.93 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.96 |
katG | 2155216 | p.Gly299Val | missense_variant | 0.91 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.9 |
PPE35 | 2168087 | c.2526G>A | synonymous_variant | 0.93 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.92 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.95 |
pepQ | 2859381 | c.1038C>G | synonymous_variant | 0.18 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086987 | p.Gln56His | missense_variant | 0.94 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3611974 | c.1143A>C | synonymous_variant | 0.12 |
fbiB | 3642877 | p.Lys448Arg | missense_variant | 0.93 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.91 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.98 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.13 |
ubiA | 4269307 | p.Phe176Ser | missense_variant | 0.13 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.92 |