Run ID: ERR2229535
Sample name:
Date: 31-03-2023 17:17:39
Number of reads: 609230
Percentage reads mapped: 99.36
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 |
---|---|---|---|---|
gyrB | 5984 | p.Arg249Ser | missense_variant | 0.12 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
fgd1 | 490744 | c.-39T>C | upstream_gene_variant | 0.12 |
fgd1 | 491129 | p.Thr116Asn | missense_variant | 0.18 |
mshA | 575924 | p.Gly193* | stop_gained | 0.25 |
mshA | 576080 | p.Asp245His | missense_variant | 0.4 |
ccsA | 620624 | p.Ile245Lys | missense_variant | 0.14 |
rpoB | 761289 | p.Ser495Ala | missense_variant | 0.33 |
rpoB | 761297 | p.Tyr497* | stop_gained | 0.4 |
rpoB | 761516 | c.1710G>T | synonymous_variant | 0.17 |
rpoB | 761879 | p.Glu691Asp | missense_variant | 0.18 |
rpoB | 762285 | p.Arg827Cys | missense_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777125 | p.Ser452Arg | missense_variant | 0.14 |
mmpL5 | 777157 | c.1324C>A | synonymous_variant | 0.2 |
mmpL5 | 777164 | c.1317C>T | synonymous_variant | 0.18 |
mmpL5 | 778431 | p.Arg17Thr | missense_variant | 0.14 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801278 | p.Pro157Leu | missense_variant | 0.2 |
fbiC | 1302764 | c.-167A>G | upstream_gene_variant | 0.12 |
fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 |
fbiC | 1304301 | c.1371C>A | synonymous_variant | 0.22 |
Rv1258c | 1406502 | p.Val280Ala | missense_variant | 0.2 |
Rv1258c | 1406931 | p.Trp137Leu | missense_variant | 0.2 |
Rv1258c | 1407089 | c.252G>T | synonymous_variant | 0.29 |
embR | 1417525 | c.-178G>C | upstream_gene_variant | 0.18 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1473058 | n.1213G>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476006 | n.2349G>A | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476705 | n.3048C>T | non_coding_transcript_exon_variant | 0.22 |
fabG1 | 1673346 | c.-94C>G | upstream_gene_variant | 0.16 |
fabG1 | 1673349 | c.-91G>C | upstream_gene_variant | 0.17 |
fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.22 |
fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.23 |
fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.23 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.28 |
fabG1 | 1674157 | p.Asp240Tyr | missense_variant | 0.15 |
rpsA | 1834205 | p.Phe222Ile | missense_variant | 0.25 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918592 | p.Leu218Pro | missense_variant | 0.15 |
ndh | 2102584 | p.Ser153Arg | missense_variant | 0.17 |
ndh | 2103186 | c.-144T>C | upstream_gene_variant | 0.11 |
katG | 2155647 | c.465C>T | synonymous_variant | 0.18 |
katG | 2155729 | p.Arg128Gln | missense_variant | 0.29 |
PPE35 | 2167814 | c.2799C>T | synonymous_variant | 0.21 |
PPE35 | 2167868 | c.2745A>C | synonymous_variant | 0.11 |
PPE35 | 2168165 | c.2448G>C | synonymous_variant | 0.29 |
PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.38 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.33 |
Rv1979c | 2221950 | c.1215T>C | synonymous_variant | 0.14 |
Rv1979c | 2222451 | c.714C>T | synonymous_variant | 0.13 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288701 | p.Glu181Lys | missense_variant | 0.22 |
pncA | 2288712 | p.Thr177Ile | missense_variant | 0.2 |
pncA | 2289380 | c.-139G>T | upstream_gene_variant | 0.25 |
pncA | 2290076 | c.-835C>A | upstream_gene_variant | 0.12 |
kasA | 2518394 | p.Leu94Ile | missense_variant | 0.14 |
kasA | 2518809 | p.Lys232Arg | missense_variant | 0.25 |
eis | 2715210 | c.123C>A | synonymous_variant | 0.11 |
ahpC | 2726450 | c.258G>A | synonymous_variant | 0.15 |
ahpC | 2726757 | p.Glu189* | stop_gained | 0.12 |
folC | 2746456 | c.1143G>A | synonymous_variant | 0.25 |
thyX | 3067958 | c.-13T>C | upstream_gene_variant | 0.29 |
ald | 3086974 | p.Ala52Val | missense_variant | 0.12 |
Rv3236c | 3612741 | p.Tyr126His | missense_variant | 0.12 |
fbiA | 3640448 | c.-95A>T | upstream_gene_variant | 0.2 |
fbiA | 3640480 | c.-63C>A | upstream_gene_variant | 0.18 |
fbiB | 3641871 | p.Val113Ile | missense_variant | 0.18 |
clpC1 | 4039418 | c.1287C>T | synonymous_variant | 0.17 |
clpC1 | 4039645 | p.His354Asp | missense_variant | 0.2 |
clpC1 | 4039654 | p.Thr351Ser | missense_variant | 0.2 |
clpC1 | 4040144 | c.561G>C | synonymous_variant | 0.15 |
embC | 4239691 | c.-172G>T | upstream_gene_variant | 0.12 |
embC | 4240409 | p.Pro183Ala | missense_variant | 0.18 |
embC | 4242047 | p.Ser729Pro | missense_variant | 0.33 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242704 | p.Asp948Asn | missense_variant | 0.17 |
embB | 4245563 | c.-951G>T | upstream_gene_variant | 0.17 |
embB | 4246082 | c.-432T>C | upstream_gene_variant | 0.2 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.5 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.5 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.33 |
embB | 4247601 | p.Leu363Arg | missense_variant | 0.14 |
aftB | 4266972 | p.Gly622Asp | missense_variant | 0.25 |
aftB | 4267135 | p.Cys568Arg | missense_variant | 0.15 |
aftB | 4267303 | p.Asn512Asp | missense_variant | 0.12 |
ubiA | 4269969 | c.-136G>T | upstream_gene_variant | 0.12 |
ethA | 4327382 | p.Ser31Ile | missense_variant | 0.18 |
ethA | 4327771 | c.-298G>A | upstream_gene_variant | 0.11 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448497 | c.-6_*1408del | transcript_ablation | 1.0 |