Run ID: ERR4828349
Sample name:
Date: 01-04-2023 18:49:20
Number of reads: 1395154
Percentage reads mapped: 99.25
Strain: lineage1.1.1.1
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 | 0.99 |
lineage1.1.1 | Indo-Oceanic | EAI4;EAI5 | RD239 | 0.99 |
lineage1.1.1.1 | Indo-Oceanic | EAI4;ZERO | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6140 | p.Val301Met | missense_variant | 0.11 |
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 | 8650 | p.Arg450His | missense_variant | 0.13 |
gyrA | 8849 | c.1548C>G | synonymous_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490972 | p.Arg64Ser | missense_variant | 1.0 |
fgd1 | 491156 | p.Phe125Cys | missense_variant | 0.17 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575320 | c.-28C>G | upstream_gene_variant | 1.0 |
rpoB | 760725 | p.Arg307Cys | missense_variant | 0.15 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.93 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764507 | p.Ala380Thr | missense_variant | 0.12 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775723 | p.Ile920Val | missense_variant | 0.11 |
mmpL5 | 775724 | c.2757G>C | synonymous_variant | 0.11 |
mmpL5 | 775937 | c.2544G>A | synonymous_variant | 0.12 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776916 | p.Met522Lys | missense_variant | 0.12 |
mmpL5 | 777136 | p.Met449Leu | missense_variant | 0.11 |
mmpL5 | 777581 | p.Tyr300* | stop_gained | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781420 | c.-140C>T | upstream_gene_variant | 0.12 |
rplC | 801100 | p.Gly98Arg | missense_variant | 1.0 |
Rv1258c | 1406182 | p.Ile387Phe | missense_variant | 0.12 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474709 | n.1052G>T | non_coding_transcript_exon_variant | 1.0 |
rpsA | 1834319 | p.Val260Ile | missense_variant | 1.0 |
rpsA | 1834379 | p.Gln280* | stop_gained | 0.22 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102469 | p.Leu192Met | missense_variant | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155445 | p.Val223Met | missense_variant | 0.12 |
katG | 2156389 | c.-278G>C | upstream_gene_variant | 1.0 |
PPE35 | 2167865 | c.2748G>C | synonymous_variant | 0.1 |
PPE35 | 2167878 | p.Ser912Asn | missense_variant | 0.12 |
PPE35 | 2167918 | c.2694T>C | synonymous_variant | 0.12 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2169605 | c.1008T>C | synonymous_variant | 0.2 |
PPE35 | 2170086 | p.Ala176Gly | missense_variant | 0.11 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518071 | c.-44G>A | upstream_gene_variant | 0.12 |
kasA | 2518123 | c.9G>A | synonymous_variant | 0.12 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
eis | 2714140 | p.Thr398Asn | missense_variant | 1.0 |
eis | 2714914 | p.Leu140Pro | missense_variant | 0.14 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
pepQ | 2860144 | p.Val92Gly | missense_variant | 0.2 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
Rv2752c | 3065143 | p.Gly350Glu | missense_variant | 1.0 |
thyX | 3068133 | c.-188G>A | upstream_gene_variant | 0.14 |
thyA | 3074229 | c.243C>T | synonymous_variant | 0.12 |
ald | 3086780 | c.-40T>C | upstream_gene_variant | 0.11 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.17 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3448794 | c.291G>A | synonymous_variant | 0.14 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474054 | c.48C>T | synonymous_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fbiA | 3640359 | c.-184C>T | upstream_gene_variant | 0.18 |
rpoA | 3878630 | c.-124delC | upstream_gene_variant | 1.0 |
clpC1 | 4040027 | c.678C>G | synonymous_variant | 0.1 |
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 | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4244096 | c.864C>T | synonymous_variant | 0.96 |
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 | 4326477 | c.997C>T | synonymous_variant | 0.14 |
whiB6 | 4338242 | p.Gln94Glu | missense_variant | 1.0 |
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 | 4407873 | c.330G>T | synonymous_variant | 1.0 |