Run ID: ERR216904
Sample name:
Date: 31-03-2023 15:55:13
Number of reads: 1292870
Percentage reads mapped: 97.71
Strain: lineage1.1.3.2
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 1.0 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 1.0 |
lineage1.1.3.2 | Indo-Oceanic | NA | RD239 | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8188 | p.Leu296Pro | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
ccsA | 619695 | c.-196G>A | upstream_gene_variant | 1.0 |
rpoB | 759628 | c.-179C>A | upstream_gene_variant | 0.11 |
rpoB | 760540 | p.Arg245Gln | missense_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.97 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 765230 | p.Ala621Thr | missense_variant | 1.0 |
rpoC | 766433 | p.Glu1022* | stop_gained | 0.12 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801166 | p.Gly120Ser | missense_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1673868 | c.-334C>T | upstream_gene_variant | 1.0 |
inhA | 1674883 | p.Ile228Val | missense_variant | 1.0 |
inhA | 1674952 | p.Pro251Ala | missense_variant | 0.3 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2153933 | p.Ala727Ser | missense_variant | 0.23 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.94 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289894 | c.-653G>T | upstream_gene_variant | 0.14 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726338 | p.Val49Gly | missense_variant | 0.4 |
folC | 2747111 | p.Phe163Ser | missense_variant | 0.11 |
pepQ | 2859652 | p.Ala256Glu | missense_variant | 0.16 |
ribD | 2987323 | p.Val162Gly | missense_variant | 0.36 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3449149 | p.Tyr216His | missense_variant | 0.1 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474271 | p.Gln89Lys | missense_variant | 0.12 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fbiB | 3642173 | c.639G>A | synonymous_variant | 1.0 |
rpoA | 3878048 | p.Ala154Thr | missense_variant | 0.11 |
rpoA | 3878687 | c.-180A>C | upstream_gene_variant | 1.0 |
clpC1 | 4038744 | p.Thr654Met | missense_variant | 0.12 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.21 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4239842 | c.-21C>A | upstream_gene_variant | 0.31 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.91 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4246771 | p.Asp86Glu | missense_variant | 0.2 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
aftB | 4267479 | p.Pro453Gln | missense_variant | 0.17 |
aftB | 4267620 | p.Gly406Asp | missense_variant | 0.15 |
ubiA | 4269381 | p.Cys151* | stop_gained | 0.12 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4327602 | c.-129C>T | upstream_gene_variant | 0.17 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407780 | c.423G>A | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |