Run ID: ERR4819152
Sample name:
Date: 01-04-2023 15:57:02
Number of reads: 744119
Percentage reads mapped: 99.78
Strain: lineage4.6.2.2
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.6 | Euro-American | T;LAM | None | 1.0 |
lineage4.6.2 | Euro-American | T;LAM | RD726 | 1.0 |
lineage4.6.2.2 | Euro-American (Cameroon) | LAM10-CAM | RD726 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5452 | p.Glu71Asp | missense_variant | 0.12 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7655 | c.354G>T | synonymous_variant | 0.13 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9411 | c.2110C>A | synonymous_variant | 0.11 |
fgd1 | 490647 | c.-136C>T | upstream_gene_variant | 0.11 |
fgd1 | 491311 | p.Gly177Ser | missense_variant | 0.14 |
mshA | 576759 | p.His471Arg | missense_variant | 0.12 |
rpoB | 760799 | p.Asp331Glu | missense_variant | 0.15 |
rpoB | 761585 | c.1779C>T | synonymous_variant | 0.13 |
rpoB | 761945 | c.2139G>C | synonymous_variant | 0.12 |
rpoC | 763166 | c.-204A>G | upstream_gene_variant | 0.13 |
rpoC | 763530 | p.Pro54Leu | missense_variant | 0.18 |
rpoC | 765371 | c.2002C>T | synonymous_variant | 0.12 |
rpoC | 765686 | p.Ala773Pro | missense_variant | 0.17 |
rpoC | 766051 | p.Glu894Asp | missense_variant | 0.17 |
rpoC | 766374 | p.Ser1002Tyr | missense_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777149 | c.1332C>T | synonymous_variant | 0.12 |
mmpR5 | 778298 | c.-692C>T | upstream_gene_variant | 1.0 |
mmpL5 | 779076 | c.-596G>T | upstream_gene_variant | 0.14 |
mmpL5 | 779094 | c.-614C>T | upstream_gene_variant | 0.17 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303875 | c.945G>A | synonymous_variant | 0.14 |
fbiC | 1305317 | p.Thr796Ile | missense_variant | 0.14 |
Rv1258c | 1407068 | c.273G>C | synonymous_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471660 | n.-185delC | upstream_gene_variant | 0.12 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.4 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918023 | c.84C>T | synonymous_variant | 0.13 |
ndh | 2102517 | p.Val176Phe | missense_variant | 0.12 |
katG | 2155389 | c.723C>G | synonymous_variant | 1.0 |
katG | 2156519 | c.-408T>C | upstream_gene_variant | 0.11 |
PPE35 | 2169191 | c.1422G>A | synonymous_variant | 0.29 |
PPE35 | 2170394 | c.219G>C | synonymous_variant | 0.11 |
Rv1979c | 2221746 | c.1416_1418dupCCG | disruptive_inframe_insertion | 0.92 |
Rv1979c | 2221845 | c.1320G>T | synonymous_variant | 0.15 |
Rv1979c | 2221922 | p.Lys415Glu | missense_variant | 0.13 |
Rv1979c | 2221956 | c.1209A>G | synonymous_variant | 0.11 |
Rv1979c | 2223065 | c.100C>T | synonymous_variant | 0.13 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290129 | c.-890_-889delGC | upstream_gene_variant | 0.18 |
kasA | 2517980 | c.-135C>A | upstream_gene_variant | 0.18 |
eis | 2714161 | p.Ala391Val | missense_variant | 0.2 |
eis | 2714692 | p.Ser214* | stop_gained | 0.12 |
folC | 2746243 | c.1356C>T | synonymous_variant | 0.15 |
folC | 2747721 | c.-123C>G | upstream_gene_variant | 0.18 |
Rv2752c | 3065022 | c.1170G>A | synonymous_variant | 0.12 |
Rv2752c | 3067124 | c.-933G>A | upstream_gene_variant | 0.18 |
thyX | 3067474 | p.Pro158Ala | missense_variant | 1.0 |
ald | 3086864 | c.45G>A | synonymous_variant | 0.12 |
Rv3083 | 3448567 | p.His22Asp | missense_variant | 1.0 |
Rv3083 | 3448843 | p.Cys114Arg | missense_variant | 0.17 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474453 | c.447G>A | synonymous_variant | 0.12 |
fprA | 3475077 | c.1071C>T | synonymous_variant | 0.18 |
whiB7 | 3568792 | c.-113C>A | upstream_gene_variant | 0.14 |
Rv3236c | 3612571 | c.546C>T | synonymous_variant | 1.0 |
Rv3236c | 3612910 | p.Leu69Phe | missense_variant | 1.0 |
Rv3236c | 3613070 | p.Ala16Val | missense_variant | 0.11 |
fbiA | 3640510 | c.-33G>A | upstream_gene_variant | 0.14 |
clpC1 | 4040793 | c.-89G>A | upstream_gene_variant | 0.13 |
panD | 4043967 | c.315C>T | synonymous_variant | 0.13 |
embC | 4240552 | c.690G>A | synonymous_variant | 0.11 |
embC | 4241135 | p.Val425Leu | missense_variant | 0.14 |
embC | 4242035 | p.Gln725Glu | missense_variant | 0.2 |
embA | 4242550 | c.-683C>G | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244882 | p.Trp550Cys | missense_variant | 0.25 |
embA | 4245149 | c.1917C>T | synonymous_variant | 0.11 |
aftB | 4267272 | p.Lys522Arg | missense_variant | 1.0 |
aftB | 4268284 | p.Val185Leu | missense_variant | 0.12 |
aftB | 4268562 | p.Leu92Pro | missense_variant | 0.17 |
ubiA | 4269477 | p.Met119Ile | missense_variant | 0.12 |
ubiA | 4269488 | p.Gly116Ser | missense_variant | 0.11 |
ubiA | 4269985 | c.-152T>C | upstream_gene_variant | 0.1 |
ethR | 4326739 | c.-810G>C | upstream_gene_variant | 1.0 |
ethR | 4327961 | p.Trp138Leu | missense_variant | 0.25 |
ethR | 4327983 | p.Trp145* | stop_gained | 0.15 |
ethA | 4328004 | c.-531C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338582 | c.-61G>A | upstream_gene_variant | 0.11 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |