Run ID: ERR2229628
Sample name:
Date: 31-03-2023 17:22:39
Number of reads: 1005060
Percentage reads mapped: 99.08
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 |
fgd1 | 491518 | p.Thr246Ala | missense_variant | 0.12 |
fgd1 | 491529 | p.Trp249* | stop_gained | 0.13 |
mshA | 575630 | p.Ser95Pro | missense_variant | 0.25 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.18 |
mshA | 576747 | p.Gly467Asp | missense_variant | 0.12 |
ccsA | 620832 | c.942C>T | synonymous_variant | 0.12 |
rpoB | 760573 | c.769delG | frameshift_variant | 0.13 |
rpoB | 760794 | p.Glu330Lys | missense_variant | 0.29 |
rpoB | 761152 | p.Leu449Gln | missense_variant | 0.2 |
rpoB | 763216 | p.Ala1137Glu | missense_variant | 0.12 |
rpoC | 765496 | c.2127C>A | synonymous_variant | 0.14 |
rpoC | 766146 | p.Gly926Ala | missense_variant | 0.11 |
rpoC | 766787 | p.Glu1140Lys | missense_variant | 0.15 |
rpoC | 766796 | p.Arg1143Ser | missense_variant | 0.15 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776018 | c.2463G>C | synonymous_variant | 0.12 |
mmpL5 | 776021 | c.2460G>C | synonymous_variant | 0.12 |
mmpL5 | 777164 | c.1317C>T | synonymous_variant | 0.12 |
mmpL5 | 777753 | c.727delA | frameshift_variant | 0.14 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801000 | c.192G>A | synonymous_variant | 0.2 |
rplC | 801110 | p.Leu101Ser | missense_variant | 0.18 |
fbiC | 1302942 | c.12T>C | synonymous_variant | 0.14 |
fbiC | 1303493 | p.Leu188Ser | missense_variant | 0.12 |
fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 |
fbiC | 1303941 | c.1011G>T | synonymous_variant | 0.5 |
fbiC | 1304335 | p.Ala469Ser | missense_variant | 0.13 |
Rv1258c | 1406252 | c.1089T>A | synonymous_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1474026 | n.369C>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474402 | n.745T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475088 | n.1431A>T | non_coding_transcript_exon_variant | 0.18 |
fabG1 | 1673346 | c.-94C>G | upstream_gene_variant | 0.12 |
fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.12 |
fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.12 |
fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.12 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.26 |
inhA | 1674586 | p.Ser129Pro | missense_variant | 0.2 |
inhA | 1674600 | c.399G>C | synonymous_variant | 0.2 |
rpsA | 1834468 | c.927A>T | synonymous_variant | 0.18 |
rpsA | 1834806 | p.Glu422Gly | missense_variant | 0.17 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102663 | p.Gly127Asp | missense_variant | 0.17 |
katG | 2154863 | p.His417Tyr | missense_variant | 0.14 |
PPE35 | 2167973 | c.2640A>G | synonymous_variant | 0.14 |
PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 |
PPE35 | 2169269 | c.1344A>G | synonymous_variant | 0.16 |
PPE35 | 2169272 | c.1341C>G | synonymous_variant | 0.16 |
PPE35 | 2169278 | c.1335T>C | synonymous_variant | 0.18 |
PPE35 | 2169281 | c.1332T>G | synonymous_variant | 0.18 |
PPE35 | 2169748 | p.Ile289Phe | missense_variant | 0.12 |
PPE35 | 2169749 | c.864A>C | synonymous_variant | 0.12 |
PPE35 | 2169902 | c.711G>C | synonymous_variant | 0.13 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.42 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.39 |
Rv1979c | 2223073 | p.Gly31Asp | missense_variant | 0.22 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518045 | c.-70G>A | upstream_gene_variant | 0.13 |
kasA | 2519057 | p.Thr315Ser | missense_variant | 0.14 |
kasA | 2519062 | c.948T>G | synonymous_variant | 0.14 |
kasA | 2519065 | c.951C>A | synonymous_variant | 0.14 |
kasA | 2519066 | c.956_982delACGCCGCGGAGGCCAACGCCATCCGCG | disruptive_inframe_deletion | 0.13 |
kasA | 2519140 | c.1026G>C | synonymous_variant | 0.18 |
kasA | 2519143 | c.1029G>C | synonymous_variant | 0.18 |
kasA | 2519283 | p.Arg390His | missense_variant | 0.13 |
eis | 2714653 | p.Arg227Pro | missense_variant | 0.22 |
eis | 2714667 | c.666G>A | synonymous_variant | 0.18 |
eis | 2714763 | c.570G>A | synonymous_variant | 0.25 |
folC | 2746587 | c.1012C>A | synonymous_variant | 0.2 |
folC | 2747175 | p.Ala142Ser | missense_variant | 0.14 |
ribD | 2986970 | p.Asn44Lys | missense_variant | 0.2 |
Rv2752c | 3064771 | p.Ala474Glu | missense_variant | 0.22 |
Rv2752c | 3065826 | c.366A>T | synonymous_variant | 0.11 |
Rv2752c | 3065985 | c.207C>T | synonymous_variant | 0.12 |
thyX | 3067442 | c.504C>A | synonymous_variant | 0.13 |
thyX | 3068031 | c.-86A>G | upstream_gene_variant | 0.11 |
fbiD | 3339270 | c.153G>T | synonymous_variant | 0.15 |
fbiD | 3339589 | p.Leu158Val | missense_variant | 0.14 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.18 |
fprA | 3474110 | p.Ala35Asp | missense_variant | 0.12 |
Rv3236c | 3612076 | c.1041G>T | synonymous_variant | 0.12 |
Rv3236c | 3613217 | c.-101G>T | upstream_gene_variant | 0.13 |
fbiB | 3642467 | c.933T>C | synonymous_variant | 0.14 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.17 |
alr | 3841612 | c.-193_-192insC | upstream_gene_variant | 0.16 |
rpoA | 3877606 | p.Leu301Pro | missense_variant | 0.12 |
clpC1 | 4038639 | p.Asp689Gly | missense_variant | 0.13 |
clpC1 | 4039042 | p.Ser555Thr | missense_variant | 0.15 |
clpC1 | 4039682 | c.1023C>T | synonymous_variant | 0.13 |
clpC1 | 4039691 | c.1014G>C | synonymous_variant | 0.11 |
clpC1 | 4039714 | p.Tyr331His | missense_variant | 0.24 |
clpC1 | 4040464 | c.240delT | frameshift_variant | 0.12 |
embC | 4242234 | p.Pro791His | missense_variant | 0.18 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243607 | c.375G>T | synonymous_variant | 0.15 |
embA | 4244807 | c.1575G>T | synonymous_variant | 0.18 |
embA | 4246204 | p.Arg991Gln | missense_variant | 0.2 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.25 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.56 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.62 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.54 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.5 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.44 |
embB | 4246709 | p.Ser66Gly | missense_variant | 0.17 |
embB | 4249766 | p.Arg1085Gly | missense_variant | 0.17 |
aftB | 4268892 | c.-56T>C | upstream_gene_variant | 0.17 |
aftB | 4269590 | c.-754C>A | upstream_gene_variant | 0.2 |
ethR | 4326961 | c.-588G>C | upstream_gene_variant | 0.12 |
ethR | 4326970 | c.-579G>T | upstream_gene_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |