Run ID: SRR1175075
Sample name:
Date: 03-04-2023 03:37:24
Number of reads: 459457
Percentage reads mapped: 91.69
Strain: lineage3.1.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.99 |
lineage3.1.1 | East-African-Indian | CAS1-Kili | RD750 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761140 | p.His445Arg | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289038 | p.Trp68Cys | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
gid | 4408095 | c.107delT | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5366 | p.His43Asp | missense_variant | 0.4 |
gyrA | 7286 | c.-16T>C | upstream_gene_variant | 0.13 |
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 | 1.0 |
ccsA | 619763 | c.-128C>G | upstream_gene_variant | 0.22 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoB | 760581 | p.Asp259Asn | missense_variant | 1.0 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763061 | c.-309C>A | upstream_gene_variant | 0.18 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpR5 | 779060 | p.Gly24Asp | missense_variant | 0.14 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302756 | c.-175G>T | upstream_gene_variant | 0.29 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1473297 | n.1452G>C | non_coding_transcript_exon_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155604 | p.Asn170His | missense_variant | 0.5 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.21 |
PPE35 | 2170461 | p.Gly51Glu | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
pncA | 2289558 | c.-317C>A | upstream_gene_variant | 0.22 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
Rv2752c | 3066375 | c.-184G>A | upstream_gene_variant | 0.2 |
thyA | 3073767 | c.705G>T | synonymous_variant | 0.17 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087534 | p.Val239Phe | missense_variant | 0.29 |
fbiD | 3339553 | p.Thr146Ser | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.29 |
clpC1 | 4039251 | p.Ala485Asp | missense_variant | 0.18 |
embC | 4240172 | p.Val104Met | missense_variant | 1.0 |
embC | 4241562 | p.Arg567His | missense_variant | 1.0 |
embC | 4241853 | p.Ala664Val | missense_variant | 0.17 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ethA | 4326552 | p.Gly308Trp | missense_variant | 0.17 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |