Run ID: ERR2517304
Sample name:
Date: 31-03-2023 22:05:43
Number of reads: 4931164
Percentage reads mapped: 99.61
Strain: lineage4;La1.2.BCG
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
La1 | M.bovis | None | None | 0.6 |
La1.2 | M.bovis | None | None | 0.5 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.44 |
La1.2.BCG | M.bovis | BCG | None | 0.5 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
pncA | 2289073 | p.His57Asp | missense_variant | 0.6 | pyrazinamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5752 | c.513G>A | synonymous_variant | 0.75 |
gyrA | 6406 | c.-896C>T | upstream_gene_variant | 0.75 |
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.78 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.88 |
gyrA | 8285 | c.984C>T | synonymous_variant | 0.79 |
gyrA | 8624 | c.1323G>T | synonymous_variant | 0.83 |
gyrA | 8741 | c.1440C>T | synonymous_variant | 0.73 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.77 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.73 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.6 |
mshA | 576725 | p.Ile460Val | missense_variant | 0.48 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.58 |
rpoC | 763575 | p.Arg69Pro | missense_variant | 0.58 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.53 |
mmpL5 | 776939 | c.1542C>T | synonymous_variant | 0.61 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781568 | c.9C>T | synonymous_variant | 0.61 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 0.5 |
fbiC | 1303638 | p.Lys236Asn | missense_variant | 0.5 |
embR | 1417498 | c.-151G>A | upstream_gene_variant | 0.4 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.54 |
rpsA | 1834859 | p.Ala440Thr | missense_variant | 0.67 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102106 | p.Gly313Arg | missense_variant | 0.63 |
ndh | 2103173 | c.-132delG | upstream_gene_variant | 0.58 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.71 |
katG | 2155503 | c.609C>T | synonymous_variant | 0.55 |
katG | 2156025 | c.87C>A | synonymous_variant | 0.51 |
katG | 2156465 | c.-354C>T | upstream_gene_variant | 0.6 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.43 |
PPE35 | 2168011 | p.Ser868Arg | missense_variant | 0.56 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.58 |
PPE35 | 2168175 | p.Gln813Arg | missense_variant | 0.61 |
PPE35 | 2168814 | c.1798dupA | frameshift_variant | 0.5 |
PPE35 | 2168920 | p.Val565Phe | missense_variant | 0.48 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.5 |
ald | 3086728 | c.-92C>T | upstream_gene_variant | 0.62 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.57 |
ald | 3087084 | c.266delA | frameshift_variant | 0.46 |
Rv3083 | 3448745 | p.Ile81Ser | missense_variant | 1.0 |
Rv3083 | 3448783 | p.Val94Ile | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.53 |
fprA | 3474427 | p.Val141Ile | missense_variant | 0.54 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.51 |
rpoA | 3878630 | c.-124delC | upstream_gene_variant | 0.3 |
clpC1 | 4038403 | c.2302T>C | synonymous_variant | 0.6 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.54 |
embC | 4242029 | c.2167C>T | synonymous_variant | 0.61 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4242970 | c.-263C>T | upstream_gene_variant | 0.55 |
embA | 4244220 | c.988C>T | synonymous_variant | 0.53 |
embB | 4246551 | p.Asn13Ser | missense_variant | 0.54 |
embB | 4246864 | c.351C>T | synonymous_variant | 0.54 |
embB | 4247173 | c.660G>A | synonymous_variant | 0.57 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.55 |
aftB | 4267858 | p.Ile327Val | missense_variant | 0.6 |
aftB | 4269351 | c.-515C>T | upstream_gene_variant | 0.68 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.63 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.56 |
ubiA | 4269689 | p.Val49Ile | missense_variant | 0.61 |
ubiA | 4269864 | c.-31C>T | upstream_gene_variant | 0.43 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.73 |