Run ID: ERR2229361
Sample name:
Date: 31-03-2023 17:06:08
Number of reads: 835549
Percentage reads mapped: 98.7
Strain: lineage4.8
Drug-resistance: HR-TB
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 |
---|---|---|---|---|---|
katG | 2155165 | p.Gly316Asp | missense_variant | 0.13 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6207 | p.Ala323Val | missense_variant | 0.14 |
gyrB | 6959 | p.Gln574* | stop_gained | 0.14 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 8243 | p.Ile314Met | missense_variant | 0.11 |
mshA | 575363 | p.His6Asn | missense_variant | 0.18 |
mshA | 575384 | p.Ile13Val | missense_variant | 0.18 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.4 |
rpoB | 761418 | p.Ala538Thr | missense_variant | 0.15 |
rpoC | 764101 | c.732C>T | synonymous_variant | 0.18 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777157 | c.1324C>A | synonymous_variant | 0.22 |
mmpL5 | 777164 | c.1317C>T | synonymous_variant | 0.17 |
mmpL5 | 777221 | p.Tyr420* | stop_gained | 0.2 |
mmpL5 | 777449 | c.1032C>T | synonymous_variant | 0.15 |
mmpR5 | 778328 | c.-662C>T | upstream_gene_variant | 0.13 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800701 | c.-108G>T | upstream_gene_variant | 0.13 |
fbiC | 1303476 | c.546G>T | synonymous_variant | 0.22 |
fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 |
fbiC | 1304155 | p.Arg409Trp | missense_variant | 0.15 |
fbiC | 1305274 | p.Ser782Pro | missense_variant | 0.13 |
Rv1258c | 1407157 | p.Ala62Pro | missense_variant | 0.11 |
atpE | 1461043 | c.-2A>T | upstream_gene_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472790 | n.945T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.14 |
fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.15 |
fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.15 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.27 |
rpsA | 1834422 | p.Gly294Val | missense_variant | 0.25 |
rpsA | 1834562 | p.Gly341Cys | missense_variant | 0.16 |
tlyA | 1917784 | c.-156C>A | upstream_gene_variant | 0.18 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102003 | p.Ile347Thr | missense_variant | 0.11 |
ndh | 2102776 | c.267C>T | synonymous_variant | 0.17 |
ndh | 2102854 | p.Ile63Leu | missense_variant | 0.11 |
ndh | 2102857 | c.186T>C | synonymous_variant | 0.12 |
ndh | 2102875 | c.168C>T | synonymous_variant | 0.21 |
katG | 2155191 | c.921A>C | synonymous_variant | 0.21 |
PPE35 | 2167745 | p.Thr956Arg | missense_variant | 0.36 |
PPE35 | 2167859 | c.2754T>C | synonymous_variant | 0.11 |
PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 |
PPE35 | 2168976 | p.Ala546Asp | missense_variant | 0.13 |
PPE35 | 2169602 | c.1011C>A | synonymous_variant | 0.14 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.58 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.6 |
Rv1979c | 2221954 | p.His404Leu | missense_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290111 | c.-870G>T | upstream_gene_variant | 0.18 |
kasA | 2518864 | c.750G>C | synonymous_variant | 0.13 |
eis | 2715100 | p.Pro78Gln | missense_variant | 0.13 |
ahpC | 2725948 | c.-245C>A | upstream_gene_variant | 0.17 |
ahpC | 2726309 | c.117C>A | synonymous_variant | 0.13 |
ahpC | 2726374 | p.Cys61Phe | missense_variant | 0.15 |
folC | 2746229 | c.1369delG | frameshift_variant | 0.25 |
folC | 2746587 | p.Arg338Trp | missense_variant | 0.17 |
folC | 2746929 | p.Pro224Thr | missense_variant | 0.2 |
pepQ | 2860162 | p.Arg86Leu | missense_variant | 0.15 |
pepQ | 2860304 | p.Ser39Ala | missense_variant | 0.25 |
Rv2752c | 3065022 | c.1170G>T | synonymous_variant | 0.12 |
Rv2752c | 3065214 | c.978C>T | synonymous_variant | 0.15 |
Rv2752c | 3065513 | p.Arg227Trp | missense_variant | 0.14 |
thyX | 3068011 | c.-66C>T | upstream_gene_variant | 0.12 |
ald | 3087348 | p.Gly177Ser | missense_variant | 0.12 |
fbiD | 3339430 | p.Glu105Lys | missense_variant | 0.17 |
fprA | 3473917 | c.-90T>A | upstream_gene_variant | 0.17 |
fprA | 3474319 | p.Gly105Cys | missense_variant | 0.33 |
whiB7 | 3568582 | p.Pro33Gln | missense_variant | 0.12 |
whiB7 | 3568624 | p.Pro19Leu | missense_variant | 0.12 |
Rv3236c | 3612693 | p.Arg142Gly | missense_variant | 0.15 |
fbiA | 3641307 | p.Met255Ile | missense_variant | 0.18 |
fbiB | 3642009 | p.Gly159Ser | missense_variant | 0.12 |
fbiB | 3642047 | c.513G>T | synonymous_variant | 0.2 |
fbiB | 3642471 | p.Met313Val | missense_variant | 0.15 |
fbiB | 3642687 | p.Leu385Val | missense_variant | 0.11 |
rpoA | 3877602 | p.His302Gln | missense_variant | 0.13 |
rpoA | 3878310 | c.198G>A | synonymous_variant | 0.12 |
clpC1 | 4038519 | p.Arg729Leu | missense_variant | 0.22 |
clpC1 | 4038575 | c.2130C>T | synonymous_variant | 0.2 |
clpC1 | 4039003 | p.Asn568Tyr | missense_variant | 0.17 |
clpC1 | 4039645 | p.His354Asp | missense_variant | 0.12 |
clpC1 | 4039654 | p.Thr351Ser | missense_variant | 0.13 |
embC | 4240651 | c.789G>T | synonymous_variant | 0.2 |
embC | 4240783 | c.921G>T | synonymous_variant | 0.12 |
embC | 4242581 | p.Ala907Ser | missense_variant | 0.22 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242725 | p.Gln955Lys | missense_variant | 0.18 |
embA | 4243440 | p.Leu70Met | missense_variant | 0.13 |
embA | 4245165 | p.Pro645Thr | missense_variant | 0.13 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.15 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.46 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.5 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.5 |
embB | 4246567 | c.54_55insT | frameshift_variant | 0.33 |
embB | 4248610 | p.Ile699Met | missense_variant | 0.25 |
embB | 4249000 | c.2487T>A | synonymous_variant | 0.18 |
aftB | 4267277 | c.1560G>T | synonymous_variant | 0.14 |
aftB | 4267910 | c.927G>A | synonymous_variant | 0.17 |
aftB | 4268658 | p.Ser60* | stop_gained | 0.25 |
ubiA | 4269208 | p.Ser209* | stop_gained | 0.25 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338705 | c.-184A>G | upstream_gene_variant | 0.11 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |