Run ID: SRR11972210
Sample name:
Date: 03-04-2023 05:32:11
Number of reads: 366527
Percentage reads mapped: 97.87
Strain: lineage1.1.3.1
Drug-resistance: Other
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 | 0.99 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 1.0 |
lineage1.1.3.1 | Indo-Oceanic | NA | RD239 | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.29 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
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 | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9566 | p.Tyr755* | stop_gained | 0.12 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576472 | c.1128delG | frameshift_variant | 0.13 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoB | 763261 | p.Ala1152Val | missense_variant | 0.14 |
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 | 766871 | p.Ile1168Val | missense_variant | 0.12 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775840 | p.Val881Leu | missense_variant | 0.18 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777572 | c.909C>T | synonymous_variant | 1.0 |
mmpR5 | 779449 | p.Leu154Met | missense_variant | 0.15 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781504 | c.-56G>A | upstream_gene_variant | 0.12 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472767 | n.922G>C | non_coding_transcript_exon_variant | 0.11 |
rpsA | 1834368 | p.Leu276His | missense_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2168313 | p.Gln767Arg | missense_variant | 0.11 |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.16 |
PPE35 | 2169910 | p.Asn235Tyr | missense_variant | 0.18 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2222911 | p.Ala85Val | missense_variant | 0.33 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289938 | c.-697T>C | upstream_gene_variant | 0.13 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
folC | 2746329 | p.Arg424Trp | missense_variant | 0.15 |
ribD | 2987608 | p.Lys257Thr | missense_variant | 1.0 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
thyX | 3067950 | c.-5G>A | upstream_gene_variant | 0.14 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
Rv3236c | 3613253 | c.-137G>A | upstream_gene_variant | 1.0 |
alr | 3840869 | c.552C>T | synonymous_variant | 0.11 |
alr | 3841253 | c.168C>T | synonymous_variant | 1.0 |
alr | 3841277 | c.144C>T | synonymous_variant | 1.0 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.18 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4242967 | c.-266C>A | upstream_gene_variant | 0.15 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4245015 | p.Ile595Val | missense_variant | 0.12 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248704 | p.Pro731Ser | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407661 | p.Ser181Leu | missense_variant | 0.15 |
gid | 4407780 | c.423G>A | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
whiB6 | 4338429 | c.-218_92del | frameshift_variant&start_lost | 1.0 |