Run ID: ERR2229766
Sample name:
Date: 31-03-2023 17:34:14
Number of reads: 549919
Percentage reads mapped: 99.16
Strain: lineage4.8
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 8094 | p.Gly265Ser | missense_variant | 0.12 |
mshA | 576368 | c.1021C>A | synonymous_variant | 0.29 |
mshA | 576404 | p.Glu353Lys | missense_variant | 0.25 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776018 | c.2463G>C | synonymous_variant | 0.18 |
mmpL5 | 776021 | c.2460G>C | synonymous_variant | 0.18 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800893 | p.Val29Phe | missense_variant | 0.33 |
fbiC | 1302969 | c.39G>A | synonymous_variant | 0.2 |
fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 |
atpE | 1460930 | c.-115C>A | upstream_gene_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473586 | n.-72G>A | upstream_gene_variant | 0.17 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475505 | n.1848G>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476162 | n.2505A>T | non_coding_transcript_exon_variant | 0.29 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.15 |
rpsA | 1833538 | c.-4C>A | upstream_gene_variant | 0.12 |
rpsA | 1833945 | p.Lys135Arg | missense_variant | 0.25 |
rpsA | 1834297 | c.756C>A | synonymous_variant | 0.18 |
tlyA | 1917816 | c.-124G>T | upstream_gene_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918640 | p.Ser234Leu | missense_variant | 0.12 |
ndh | 2101714 | p.Glu443Asp | missense_variant | 0.25 |
katG | 2156525 | c.-414T>C | upstream_gene_variant | 0.11 |
PPE35 | 2167745 | p.Thr956Arg | missense_variant | 0.18 |
PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 |
PPE35 | 2169269 | c.1344A>G | synonymous_variant | 0.18 |
PPE35 | 2169272 | c.1341C>G | synonymous_variant | 0.18 |
PPE35 | 2169278 | c.1335T>C | synonymous_variant | 0.22 |
PPE35 | 2169281 | c.1332T>G | synonymous_variant | 0.22 |
PPE35 | 2169287 | c.1326T>C | synonymous_variant | 0.19 |
PPE35 | 2169293 | c.1320T>C | synonymous_variant | 0.13 |
PPE35 | 2169308 | c.1305C>T | synonymous_variant | 0.19 |
PPE35 | 2169463 | p.Val384Leu | missense_variant | 0.15 |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.22 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.37 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.41 |
PPE35 | 2170392 | p.Gly74Ala | missense_variant | 0.15 |
PPE35 | 2170400 | c.213G>C | synonymous_variant | 0.14 |
Rv1979c | 2222887 | p.Tyr93Phe | missense_variant | 0.17 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518071 | c.-44G>T | upstream_gene_variant | 0.17 |
kasA | 2518192 | c.78G>A | synonymous_variant | 0.15 |
Rv2752c | 3065053 | p.Glu380Ala | missense_variant | 0.13 |
Rv2752c | 3066328 | c.-137T>C | upstream_gene_variant | 0.12 |
ald | 3087250 | p.Val144Asp | missense_variant | 0.12 |
fbiD | 3339324 | c.207G>A | synonymous_variant | 0.12 |
fbiD | 3339480 | c.363G>A | synonymous_variant | 0.18 |
fbiD | 3339678 | p.Cys187* | stop_gained | 0.14 |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 1.0 |
fprA | 3474143 | p.Trp46Tyr | missense_variant | 0.18 |
fprA | 3474578 | p.Ile191Thr | missense_variant | 0.12 |
fprA | 3475239 | c.1233A>G | synonymous_variant | 0.17 |
Rv3236c | 3612638 | p.Phe160Ser | missense_variant | 0.25 |
fbiB | 3640830 | c.-705C>T | upstream_gene_variant | 0.17 |
fbiA | 3640888 | c.349delC | frameshift_variant | 0.17 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.32 |
rpoA | 3878158 | c.329_349delTCGTGCCGCCGGCCGGCGTCA | disruptive_inframe_deletion | 0.18 |
rpoA | 3878182 | p.Asp109Gly | missense_variant | 0.18 |
ddn | 3987290 | c.447C>T | synonymous_variant | 0.13 |
clpC1 | 4038617 | c.2088G>A | synonymous_variant | 0.2 |
clpC1 | 4039526 | c.1179G>C | synonymous_variant | 0.2 |
clpC1 | 4039645 | p.His354Asp | missense_variant | 0.25 |
clpC1 | 4039654 | p.Thr351Ser | missense_variant | 0.23 |
embC | 4239893 | p.Ala11Ser | missense_variant | 0.29 |
embC | 4240801 | c.939C>T | synonymous_variant | 0.2 |
embC | 4240803 | p.Tyr314Phe | missense_variant | 0.2 |
embC | 4241455 | c.1593C>A | synonymous_variant | 0.13 |
embC | 4241831 | p.Trp657Arg | missense_variant | 0.33 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243905 | p.Asp225Asn | missense_variant | 0.14 |
embA | 4246200 | p.Gln990* | stop_gained | 0.17 |
embB | 4247761 | p.Tyr416* | stop_gained | 0.12 |
embB | 4249253 | p.Gly914Trp | missense_variant | 0.18 |
embB | 4249297 | c.2784G>A | synonymous_variant | 0.17 |
aftB | 4267082 | p.His585Gln | missense_variant | 0.14 |
aftB | 4267933 | p.Ala302Pro | missense_variant | 0.2 |
ubiA | 4269391 | p.Val148Glu | missense_variant | 0.15 |
ubiA | 4269413 | p.Gly141Cys | missense_variant | 0.14 |
ethR | 4326961 | c.-588G>C | upstream_gene_variant | 0.14 |
ethR | 4326964 | c.-585G>A | upstream_gene_variant | 0.13 |
ethR | 4326970 | c.-579G>T | upstream_gene_variant | 0.12 |
ethR | 4327360 | c.-189C>A | upstream_gene_variant | 0.18 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448497 | c.-6_*1408del | transcript_ablation | 1.0 |