Run ID: SRR6797810
Sample name:
Date: 04-04-2023 16:18:54
Number of reads: 3148781
Percentage reads mapped: 99.56
Strain: lineage2.2.1.2;lineage1.1.3.1
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.75 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.22 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.22 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.79 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 0.25 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.75 |
lineage1.1.3.1 | Indo-Oceanic | NA | RD239 | 0.23 |
lineage2.2.1.2 | East-Asian (Beijing) | Beijing-RD142 | RD105;RD207;RD181;RD142 | 0.81 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.17 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8292 | p.Leu331Val | missense_variant | 0.33 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.26 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.14 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.74 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.79 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.24 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.25 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.29 |
rpoC | 765230 | p.Ala621Thr | missense_variant | 0.27 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.77 |
mmpL5 | 777352 | p.Arg377Trp | missense_variant | 0.14 |
mmpL5 | 777572 | c.909C>T | synonymous_variant | 0.16 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.9 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.75 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.24 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.76 |
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 | 0.3 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.2 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.17 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.2 |
pepQ | 2860028 | c.391C>T | synonymous_variant | 0.82 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.26 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.21 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474171 | c.165G>A | synonymous_variant | 0.21 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.43 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.34 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.78 |
alr | 3841253 | c.168C>T | synonymous_variant | 0.3 |
alr | 3841277 | c.144C>T | synonymous_variant | 0.32 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.23 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.41 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.8 |
embA | 4243545 | c.313C>T | synonymous_variant | 0.33 |
embA | 4243848 | p.Val206Met | missense_variant | 0.28 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.2 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.14 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.95 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.16 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.19 |
ethA | 4326914 | p.Ala187Gly | missense_variant | 0.23 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407780 | c.423G>A | synonymous_variant | 0.21 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.12 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.83 |