Run ID: SRR1173102
Sample name:
Date: 03-04-2023 03:16:34
Number of reads: 466270
Percentage reads mapped: 87.34
Strain: lineage4.4.1.1.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.4 | Euro-American | S;T | None | 1.0 |
lineage4.4.1.1 | Euro-American | S;Orphans | None | 1.0 |
lineage4.4.1.1.1 | Euro-American | S;Orphans | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289142 | p.Tyr34Asp | missense_variant | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoB | 762888 | p.His1028Asn | missense_variant | 0.17 |
rpoC | 763371 | p.Val1Glu | missense_variant | 0.14 |
rpoC | 766487 | p.Pro1040Ser | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776689 | p.Trp598Arg | missense_variant | 0.13 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1416688 | c.660G>A | synonymous_variant | 0.2 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1833352 | c.-190C>A | upstream_gene_variant | 0.2 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102990 | p.Val18Ala | missense_variant | 1.0 |
PPE35 | 2167753 | p.Ala954Thr | missense_variant | 0.14 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.67 |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ribD | 2986827 | c.-12G>A | upstream_gene_variant | 1.0 |
Rv2752c | 3064993 | p.Trp400* | stop_gained | 1.0 |
Rv2752c | 3065439 | c.753C>G | synonymous_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339287 | p.Arg57Leu | missense_variant | 1.0 |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 1.0 |
rpoA | 3878168 | p.Ala114Thr | missense_variant | 0.4 |
clpC1 | 4038215 | c.2490G>T | synonymous_variant | 0.29 |
embC | 4240394 | p.Glu178* | stop_gained | 0.29 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243155 | c.-78G>A | upstream_gene_variant | 0.22 |
ubiA | 4269313 | p.Lys174Thr | missense_variant | 1.0 |
ethA | 4327563 | c.-90C>T | upstream_gene_variant | 0.17 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |