Run ID: ERR4819359
Sample name:
Date: 01-04-2023 16:03:55
Number of reads: 793395
Percentage reads mapped: 99.69
Strain: lineage4.3.4.2
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 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.99 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 1.0 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6866 | p.Leu543Met | missense_variant | 0.2 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7810 | c.513delC | frameshift_variant | 0.17 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491463 | p.Lys227Asn | missense_variant | 0.15 |
mshA | 576011 | p.Arg222Gly | missense_variant | 0.15 |
mshA | 576024 | p.Ser226* | stop_gained | 0.15 |
ccsA | 620703 | c.813G>A | synonymous_variant | 0.11 |
rpoB | 762474 | p.Gly890Ser | missense_variant | 0.17 |
rpoC | 763953 | p.Arg195His | missense_variant | 0.14 |
rpoC | 764953 | c.1584G>A | synonymous_variant | 0.11 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
rpoC | 766984 | c.3615G>T | synonymous_variant | 0.15 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776787 | p.Glu565Gly | missense_variant | 0.14 |
mmpL5 | 776872 | p.Glu537* | stop_gained | 0.12 |
mmpR5 | 778996 | p.Val3Ile | missense_variant | 1.0 |
mmpR5 | 779026 | p.Glu13Lys | missense_variant | 0.11 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303663 | c.733C>T | synonymous_variant | 0.2 |
fbiC | 1304483 | p.Ala518Asp | missense_variant | 0.17 |
fbiC | 1304963 | p.Trp678Leu | missense_variant | 0.15 |
embR | 1417361 | c.-14A>G | upstream_gene_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471747 | n.-99G>A | upstream_gene_variant | 0.29 |
rrs | 1472223 | n.378C>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1473615 | n.-43G>A | upstream_gene_variant | 0.17 |
rrl | 1473764 | n.107G>A | non_coding_transcript_exon_variant | 0.5 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154299 | p.Pro605Thr | missense_variant | 0.13 |
PPE35 | 2168331 | p.Leu761Pro | missense_variant | 0.11 |
PPE35 | 2169052 | p.Asn521Asp | missense_variant | 0.12 |
PPE35 | 2169617 | p.Phe332Leu | missense_variant | 0.12 |
PPE35 | 2170400 | c.213G>A | synonymous_variant | 0.17 |
PPE35 | 2170681 | c.-69G>A | upstream_gene_variant | 1.0 |
Rv1979c | 2222106 | c.1059C>T | synonymous_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289239 | c.3G>T | start_lost | 0.13 |
kasA | 2517947 | c.-168C>A | upstream_gene_variant | 0.12 |
kasA | 2518046 | c.-69C>A | upstream_gene_variant | 0.15 |
kasA | 2518195 | c.81G>A | synonymous_variant | 0.13 |
kasA | 2518201 | c.87C>T | synonymous_variant | 0.12 |
folC | 2746726 | p.Leu291Phe | missense_variant | 0.11 |
folC | 2746807 | c.792G>T | synonymous_variant | 0.13 |
Rv2752c | 3064722 | c.1470A>T | synonymous_variant | 0.11 |
Rv2752c | 3065293 | p.Val300Ala | missense_variant | 1.0 |
thyX | 3067911 | p.Ile12Thr | missense_variant | 0.15 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087441 | p.Asp208Tyr | missense_variant | 0.13 |
Rv3083 | 3448539 | c.36C>A | synonymous_variant | 0.17 |
Rv3083 | 3449137 | c.634C>A | synonymous_variant | 0.15 |
Rv3083 | 3449397 | p.Cys298* | stop_gained | 0.11 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568419 | c.261C>T | synonymous_variant | 0.13 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 |
Rv3236c | 3612812 | p.Thr102Lys | missense_variant | 0.11 |
Rv3236c | 3613264 | c.-148G>T | upstream_gene_variant | 0.12 |
fbiB | 3642787 | p.Trp418* | stop_gained | 0.12 |
alr | 3840789 | p.Gln211Arg | missense_variant | 0.11 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
clpC1 | 4040032 | p.Val225Phe | missense_variant | 0.12 |
clpC1 | 4040071 | p.Pro212Thr | missense_variant | 0.11 |
clpC1 | 4040078 | p.Lys209Asn | missense_variant | 0.12 |
panD | 4044373 | c.-92C>A | upstream_gene_variant | 0.15 |
embC | 4239763 | c.-100C>T | upstream_gene_variant | 1.0 |
embC | 4240107 | p.Leu82Ser | missense_variant | 0.14 |
embC | 4241709 | p.Arg616Gln | missense_variant | 0.22 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243209 | c.-24C>T | upstream_gene_variant | 0.11 |
embA | 4244354 | c.1122G>A | synonymous_variant | 0.14 |
embA | 4244648 | c.1416G>C | synonymous_variant | 0.12 |
embB | 4246895 | p.Arg128Ser | missense_variant | 0.14 |
embB | 4248361 | c.1848A>G | synonymous_variant | 0.15 |
aftB | 4266980 | p.Asp619Glu | missense_variant | 0.12 |
ethR | 4327723 | p.Pro59Thr | missense_variant | 0.13 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407889 | p.Val105Glu | missense_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |