Run ID: ERR2513862
Sample name:
Date: 31-03-2023 19:57:17
Number of reads: 543606
Percentage reads mapped: 99.78
Strain: lineage4.9
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 |
lineage4.9 | Euro-American (H37Rv-like) | T1 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2155783 | p.Ala110Val | missense_variant | 0.33 | isoniazid |
ethA | 4326317 | p.Tyr386Cys | missense_variant | 0.2 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5467 | c.230_232delTCG | disruptive_inframe_deletion | 0.18 |
gyrB | 6166 | c.927C>T | synonymous_variant | 1.0 |
gyrA | 6427 | c.-875T>C | upstream_gene_variant | 0.25 |
gyrB | 6767 | p.Gly510Ser | missense_variant | 0.29 |
gyrA | 7293 | c.-9G>T | upstream_gene_variant | 0.33 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 8623 | p.Arg441Leu | missense_variant | 0.14 |
gyrA | 8681 | c.1380C>T | synonymous_variant | 0.22 |
gyrA | 8924 | c.1623C>T | synonymous_variant | 0.12 |
gyrA | 9233 | c.1932C>A | synonymous_variant | 0.11 |
gyrA | 9649 | p.Val783Ala | missense_variant | 0.13 |
fgd1 | 490858 | p.Ala26Thr | missense_variant | 0.33 |
fgd1 | 490900 | p.His40Asp | missense_variant | 0.4 |
mshA | 576188 | p.Asp281Asn | missense_variant | 0.33 |
mshA | 576488 | p.Val381Leu | missense_variant | 0.18 |
ccsA | 619984 | c.94C>T | synonymous_variant | 0.22 |
ccsA | 620140 | p.Ala84Thr | missense_variant | 0.25 |
rpoB | 759620 | c.-187A>C | upstream_gene_variant | 0.27 |
rpoB | 760752 | p.Leu316Met | missense_variant | 0.12 |
rpoB | 761061 | p.Ala419Thr | missense_variant | 0.18 |
rpoB | 762166 | p.Gly787Val | missense_variant | 0.11 |
rpoC | 762560 | c.-810A>G | upstream_gene_variant | 0.17 |
rpoB | 762653 | p.Trp949Cys | missense_variant | 0.18 |
rpoC | 763378 | c.9C>T | synonymous_variant | 0.18 |
rpoC | 763842 | p.Glu158Gly | missense_variant | 0.15 |
rpoC | 764959 | c.1590G>A | synonymous_variant | 0.13 |
rpoC | 765084 | p.Arg572His | missense_variant | 0.13 |
rpoC | 765753 | p.Asp795Val | missense_variant | 0.14 |
rpoC | 766590 | p.Glu1074Val | missense_variant | 0.12 |
rpoC | 766824 | p.Lys1152Arg | missense_variant | 0.25 |
mmpL5 | 775610 | p.Ser957Phe | missense_variant | 0.14 |
mmpL5 | 777180 | p.Ala434Glu | missense_variant | 0.11 |
mmpS5 | 778799 | p.Gly36Val | missense_variant | 0.18 |
rpsL | 781682 | c.123T>C | synonymous_variant | 0.12 |
rplC | 800905 | p.Pro33Thr | missense_variant | 0.13 |
rplC | 800932 | p.Pro42Thr | missense_variant | 0.12 |
rplC | 800992 | p.Val62Phe | missense_variant | 0.15 |
rplC | 801248 | p.Arg147His | missense_variant | 0.25 |
fbiC | 1302888 | c.-43G>T | upstream_gene_variant | 0.12 |
fbiC | 1303651 | p.Arg241Trp | missense_variant | 0.18 |
fbiC | 1303673 | p.Ala248Asp | missense_variant | 0.18 |
fbiC | 1303713 | c.783C>A | synonymous_variant | 0.13 |
fbiC | 1303857 | c.927C>T | synonymous_variant | 0.33 |
fbiC | 1304801 | p.Arg624Gln | missense_variant | 0.13 |
fbiC | 1304828 | p.Phe633Ser | missense_variant | 0.11 |
fbiC | 1304990 | p.Thr687Lys | missense_variant | 0.25 |
Rv1258c | 1406139 | p.Arg401His | missense_variant | 0.12 |
Rv1258c | 1406491 | p.Arg284Ser | missense_variant | 0.18 |
Rv1258c | 1406729 | c.610_611delCG | frameshift_variant | 0.18 |
embR | 1417147 | c.201C>T | synonymous_variant | 0.18 |
atpE | 1461054 | p.Thr4Ala | missense_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475872 | n.2215A>G | non_coding_transcript_exon_variant | 0.5 |
rpsA | 1833402 | c.-140G>T | upstream_gene_variant | 0.25 |
rpsA | 1833403 | c.-139G>A | upstream_gene_variant | 0.25 |
rpsA | 1833421 | c.-121C>G | upstream_gene_variant | 0.17 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1917977 | p.Arg13Pro | missense_variant | 0.33 |
ndh | 2101846 | c.1197G>A | synonymous_variant | 0.17 |
ndh | 2102447 | p.Gly199Val | missense_variant | 0.29 |
ndh | 2102565 | p.Arg160Trp | missense_variant | 0.12 |
katG | 2154407 | p.Pro569Thr | missense_variant | 0.13 |
katG | 2155993 | p.Pro40Leu | missense_variant | 0.14 |
PPE35 | 2167865 | c.2748G>C | synonymous_variant | 0.17 |
PPE35 | 2167868 | c.2745A>C | synonymous_variant | 0.17 |
PPE35 | 2169138 | p.Thr492Lys | missense_variant | 0.15 |
PPE35 | 2169497 | c.1116C>T | synonymous_variant | 0.12 |
PPE35 | 2170286 | c.327G>A | synonymous_variant | 0.18 |
Rv1979c | 2221740 | c.1425C>T | synonymous_variant | 0.11 |
Rv1979c | 2221784 | p.Ala461Pro | missense_variant | 0.12 |
Rv1979c | 2222998 | p.Ile56Asn | missense_variant | 0.18 |
pncA | 2288708 | c.534C>T | synonymous_variant | 0.15 |
pncA | 2288801 | c.441A>G | synonymous_variant | 0.12 |
pncA | 2288905 | p.Gly113Arg | missense_variant | 0.14 |
pncA | 2290221 | c.-980C>A | upstream_gene_variant | 0.22 |
kasA | 2517935 | c.-180C>T | upstream_gene_variant | 0.18 |
kasA | 2518449 | p.Val112Ala | missense_variant | 0.13 |
kasA | 2518486 | c.372G>A | synonymous_variant | 0.12 |
kasA | 2518814 | p.Arg234Gly | missense_variant | 0.22 |
kasA | 2518915 | c.801T>C | synonymous_variant | 0.17 |
kasA | 2518976 | p.Gly288Cys | missense_variant | 0.2 |
kasA | 2519128 | c.1014G>C | synonymous_variant | 0.22 |
kasA | 2519131 | c.1017G>C | synonymous_variant | 0.33 |
kasA | 2519140 | c.1026G>C | synonymous_variant | 0.33 |
kasA | 2519143 | c.1029G>C | synonymous_variant | 0.33 |
eis | 2714130 | p.Glu401Asp | missense_variant | 0.14 |
ahpC | 2726234 | p.Gln14His | missense_variant | 0.11 |
folC | 2746153 | c.1446C>T | synonymous_variant | 0.14 |
folC | 2746829 | p.Ala257Val | missense_variant | 0.17 |
pepQ | 2859440 | p.Gly327Ser | missense_variant | 0.22 |
pepQ | 2859940 | p.Arg160Pro | missense_variant | 1.0 |
ribD | 2986732 | c.-107C>T | upstream_gene_variant | 0.15 |
ribD | 2986856 | p.Gln6His | missense_variant | 0.11 |
Rv2752c | 3065375 | p.Ala273Ser | missense_variant | 0.67 |
Rv2752c | 3066241 | c.-50C>T | upstream_gene_variant | 0.12 |
thyX | 3067320 | p.Arg209Gln | missense_variant | 0.33 |
thyX | 3068052 | c.-107C>A | upstream_gene_variant | 0.22 |
thyA | 3073975 | p.Arg166His | missense_variant | 0.11 |
thyA | 3074343 | c.129G>T | synonymous_variant | 0.13 |
thyA | 3074648 | c.-177T>G | upstream_gene_variant | 0.25 |
ald | 3087203 | c.384C>A | synonymous_variant | 0.18 |
Rv3083 | 3448975 | p.Arg158Trp | missense_variant | 0.29 |
Rv3083 | 3449502 | c.999C>T | synonymous_variant | 0.11 |
Rv3083 | 3449825 | p.Ser441Tyr | missense_variant | 0.12 |
Rv3083 | 3449868 | c.1365C>T | synonymous_variant | 0.12 |
whiB7 | 3568673 | p.Val3Leu | missense_variant | 0.22 |
Rv3236c | 3612910 | p.Leu69Phe | missense_variant | 0.18 |
Rv3236c | 3613132 | c.-16G>T | upstream_gene_variant | 0.15 |
fbiA | 3640352 | c.-191G>A | upstream_gene_variant | 0.12 |
fbiA | 3640417 | c.-126C>T | upstream_gene_variant | 0.13 |
fbiB | 3640674 | c.-861C>T | upstream_gene_variant | 0.13 |
fbiB | 3641702 | c.168C>T | synonymous_variant | 0.29 |
fbiB | 3641830 | p.Leu99Pro | missense_variant | 0.22 |
alr | 3840458 | c.963G>T | synonymous_variant | 0.2 |
alr | 3840926 | p.Asn165Lys | missense_variant | 0.25 |
alr | 3841230 | p.Val64Glu | missense_variant | 0.14 |
rpoA | 3877961 | p.Val183Ile | missense_variant | 0.18 |
clpC1 | 4038379 | p.Thr776Ala | missense_variant | 0.15 |
clpC1 | 4038720 | p.Leu662Pro | missense_variant | 0.11 |
clpC1 | 4039958 | c.747G>T | synonymous_variant | 0.11 |
clpC1 | 4040071 | p.Pro212Thr | missense_variant | 0.25 |
clpC1 | 4040178 | c.526delC | frameshift_variant | 0.11 |
panD | 4044072 | c.210C>A | synonymous_variant | 0.17 |
embC | 4240517 | p.Asp219Asn | missense_variant | 0.2 |
embC | 4240746 | p.Gly295Asp | missense_variant | 0.11 |
embC | 4241476 | c.1614G>A | synonymous_variant | 0.13 |
embC | 4241941 | c.2079A>C | synonymous_variant | 0.15 |
embA | 4243463 | c.231G>T | synonymous_variant | 0.14 |
embA | 4244049 | p.Asp273Asn | missense_variant | 0.12 |
embB | 4247383 | p.Trp290Cys | missense_variant | 0.14 |
embB | 4248489 | p.Ala659Val | missense_variant | 0.13 |
embB | 4248719 | p.Gly736Arg | missense_variant | 0.22 |
embB | 4249063 | c.2550C>T | synonymous_variant | 0.14 |
aftB | 4267085 | c.1752G>A | synonymous_variant | 0.12 |
aftB | 4267285 | p.Thr518Ala | missense_variant | 0.13 |
aftB | 4269171 | c.-335C>T | upstream_gene_variant | 1.0 |
ubiA | 4269773 | p.Ile21Val | missense_variant | 0.18 |
ethA | 4326387 | p.Ile363Phe | missense_variant | 0.13 |
ethA | 4326999 | p.Gly159Trp | missense_variant | 0.15 |
ethR | 4327324 | c.-225A>G | upstream_gene_variant | 0.11 |
ethR | 4327414 | c.-135G>A | upstream_gene_variant | 0.13 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407542 | p.Gly221Arg | missense_variant | 0.25 |
gid | 4408063 | p.Arg47Gln | missense_variant | 1.0 |