Run ID: ERR4828589
Sample name:
Date: 01-04-2023 18:58:19
Number of reads: 987435
Percentage reads mapped: 99.35
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 | 1.0 |
lineage1.1.1 | Indo-Oceanic | EAI4;EAI5 | RD239 | 1.0 |
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 | 5887 | p.Asp216Glu | missense_variant | 0.11 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6539 | p.Asp434Asn | missense_variant | 0.14 |
gyrA | 6604 | c.-698G>A | upstream_gene_variant | 0.13 |
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 | 8454 | p.Asn385Asp | missense_variant | 0.1 |
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 | 491742 | c.960T>C | synonymous_variant | 1.0 |
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 | 765320 | p.Phe651Leu | missense_variant | 0.13 |
rpoC | 766878 | p.Ser1170Leu | missense_variant | 0.22 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777581 | p.Tyr300* | stop_gained | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406278 | p.Leu355Val | missense_variant | 0.13 |
Rv1258c | 1406519 | c.822A>T | synonymous_variant | 0.13 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
embR | 1417305 | c.43C>T | synonymous_variant | 0.14 |
embR | 1417438 | c.-91G>T | upstream_gene_variant | 0.2 |
atpE | 1461266 | c.223delG | frameshift_variant | 0.14 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472724 | n.879G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474709 | n.1052G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476244 | n.2587G>T | non_coding_transcript_exon_variant | 0.13 |
rpsA | 1833941 | p.Val134Phe | missense_variant | 0.14 |
rpsA | 1834200 | p.Val220Asp | missense_variant | 0.14 |
rpsA | 1834319 | p.Val260Ile | missense_variant | 1.0 |
rpsA | 1834405 | c.864C>T | synonymous_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154181 | p.Gly644Val | missense_variant | 0.13 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2156389 | c.-278G>C | upstream_gene_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2168565 | p.Pro683Leu | missense_variant | 0.13 |
PPE35 | 2169434 | c.1179C>T | synonymous_variant | 0.17 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2222922 | c.243C>T | synonymous_variant | 0.14 |
Rv1979c | 2223033 | c.132A>G | synonymous_variant | 0.11 |
Rv1979c | 2223114 | c.51C>T | synonymous_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290064 | c.-823C>T | upstream_gene_variant | 0.15 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
Rv2752c | 3065100 | c.1092C>A | synonymous_variant | 0.19 |
thyA | 3074169 | p.Trp101Phe | missense_variant | 0.12 |
ald | 3086690 | c.-130G>A | upstream_gene_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087630 | p.Gln271* | stop_gained | 0.2 |
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 | 3568467 | c.213C>T | synonymous_variant | 0.12 |
fbiA | 3640344 | c.-199C>T | upstream_gene_variant | 0.15 |
alr | 3840442 | p.Glu327Lys | missense_variant | 0.15 |
rpoA | 3878186 | p.Gly108Arg | missense_variant | 0.13 |
rpoA | 3878187 | c.321C>A | synonymous_variant | 0.13 |
rpoA | 3878630 | c.-124delC | upstream_gene_variant | 1.0 |
clpC1 | 4039201 | p.Ala502Thr | missense_variant | 1.0 |
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 | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4249761 | p.Ala1083Gly | missense_variant | 0.11 |
aftB | 4268310 | p.Ala176Val | missense_variant | 0.13 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4327254 | p.Ala74Thr | missense_variant | 0.17 |
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 |