Run ID: SRR19428585
Sample name:
Date: 03-04-2023 21:40:59
Number of reads: 1828128
Percentage reads mapped: 99.59
Strain: lineage4.6.1.1;lineage4.3;lineage3.1.1;lineage1.1.2
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.68 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.14 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.07 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.06 |
lineage4.6 | Euro-American | T;LAM | None | 0.1 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.12 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 0.37 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 0.06 |
lineage3.1.1 | East-African-Indian | CAS1-Kili | RD750 | 0.41 |
lineage4.6.1.1 | Euro-American | T2-Uganda | RD724 | 0.09 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.7 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.42 |
rpoB | 760948 | p.Asn381Ser | missense_variant | 0.12 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.65 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.81 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.14 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.12 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.9 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1305494 | c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT | frameshift_variant&stop_lost&splice_region_variant | 0.27 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472857 | n.1012A>G | non_coding_transcript_exon_variant | 0.3 |
tlyA | 1917777 | c.-163A>G | upstream_gene_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.72 |
katG | 2155557 | c.555C>T | synonymous_variant | 0.11 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.84 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.17 |
PPE35 | 2170461 | p.Gly51Glu | missense_variant | 0.33 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.44 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.7 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.16 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.14 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.7 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.15 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.15 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.92 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612870 | p.Ala83Ser | missense_variant | 0.28 |
fbiB | 3642098 | c.564G>A | synonymous_variant | 0.44 |
alr | 3840636 | p.Pro262Gln | missense_variant | 0.2 |
rpoA | 3878622 | c.-115C>G | upstream_gene_variant | 0.6 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.17 |
embC | 4240172 | p.Val104Met | missense_variant | 0.11 |
embC | 4241562 | p.Arg567His | missense_variant | 0.29 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.52 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 0.12 |
embA | 4245883 | p.Gly884Asp | missense_variant | 0.3 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.12 |
ethA | 4328329 | c.-856C>G | upstream_gene_variant | 0.15 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.79 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.11 |
fbiC | 1305494 | c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | frameshift_variant&stop_lost&splice_region_variant | 1.0 |