Run ID: SRR6797512
Sample name:
Date: 04-04-2023 16:11:23
Number of reads: 878087
Percentage reads mapped: 97.98
Strain: lineage1.1.3.1
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 | 0.99 |
lineage1.1.3.1 | Indo-Oceanic | NA | RD239 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5501 | p.Thr88Ser | missense_variant | 0.15 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 7251 | p.Arg671Gln | missense_variant | 0.12 |
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 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
ccsA | 620653 | c.767delG | frameshift_variant | 0.13 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
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 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpS5 | 779526 | c.-621G>A | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304578 | p.Arg550Cys | missense_variant | 0.14 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471981 | n.136C>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476408 | n.2751G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476413 | n.2756A>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476414 | n.2757T>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476430 | n.2773G>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476433 | n.2776C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.12 |
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 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290055 | c.-814A>G | upstream_gene_variant | 0.22 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
folC | 2746189 | c.1410C>G | synonymous_variant | 0.14 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
Rv2752c | 3067166 | c.-975G>A | upstream_gene_variant | 0.14 |
ald | 3086727 | c.-93G>A | upstream_gene_variant | 0.17 |
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 |
whiB7 | 3568738 | c.-59C>A | upstream_gene_variant | 0.13 |
alr | 3841253 | c.168C>T | synonymous_variant | 1.0 |
clpC1 | 4038839 | c.1866G>T | synonymous_variant | 0.12 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
panD | 4044065 | p.Gly73Ser | missense_variant | 0.12 |
panD | 4044086 | p.Ser66Gly | missense_variant | 0.15 |
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 | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4327034 | p.Tyr147Cys | missense_variant | 0.15 |
ethR | 4327360 | c.-189C>T | upstream_gene_variant | 0.14 |
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 |
whiB6 | 4338429 | c.-218_92del | frameshift_variant&start_lost | 1.0 |