Run ID: ERR036224
Sample name:
Date: 31-03-2023 08:30:38
Number of reads: 1096221
Percentage reads mapped: 95.69
Strain: lineage4.3.4.2.1;lineage1.1.3
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.72 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.16 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.64 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.23 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 0.08 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.38 |
lineage4.3.4.2.1 | Euro-American (LAM) | LAM11 | RD174 | 0.39 |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.17 |
gyrB | 6140 | p.Val301Leu | missense_variant | 0.38 |
gyrA | 6445 | c.-857C>T | upstream_gene_variant | 0.11 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7493 | c.192C>T | synonymous_variant | 0.21 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.89 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 0.12 |
gyrA | 8188 | p.Leu296Pro | missense_variant | 0.17 |
gyrA | 8377 | p.Asp359Gly | missense_variant | 0.29 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.15 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.16 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.76 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.23 |
ccsA | 619695 | c.-196G>A | upstream_gene_variant | 0.24 |
ccsA | 620029 | c.139C>T | synonymous_variant | 0.18 |
ccsA | 620407 | p.Pro173Ala | missense_variant | 0.37 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.12 |
rpoB | 759608 | c.-199C>T | upstream_gene_variant | 0.13 |
rpoB | 762249 | p.Leu815Val | missense_variant | 0.14 |
rpoC | 762836 | c.-534C>G | upstream_gene_variant | 0.25 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.3 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.42 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.11 |
rpoC | 765230 | p.Ala621Thr | missense_variant | 0.2 |
rpoC | 767305 | p.Tyr1312* | stop_gained | 0.25 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777745 | p.Gly246Ser | missense_variant | 0.15 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800997 | p.Asn63Lys | missense_variant | 0.36 |
rplC | 801166 | p.Gly120Ser | missense_variant | 0.25 |
Rv1258c | 1407055 | c.285delG | frameshift_variant | 0.15 |
Rv1258c | 1407240 | p.Val34Gly | missense_variant | 0.38 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.15 |
embR | 1417501 | c.-154A>C | upstream_gene_variant | 0.43 |
atpE | 1461019 | c.-26C>A | upstream_gene_variant | 0.28 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472203 | n.358G>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472213 | n.368G>C | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472378 | n.533G>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472379 | n.534T>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472400 | n.555C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472415 | n.570T>G | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473343 | n.1498G>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1473352 | n.1507C>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1474380 | n.723G>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475363 | n.1706C>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476225 | n.2568T>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.34 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.12 |
inhA | 1674892 | p.Asn231Asp | missense_variant | 0.4 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.23 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918106 | p.Thr56Ile | missense_variant | 0.15 |
ndh | 2102891 | p.Phe51Ser | missense_variant | 0.35 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.36 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.36 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.33 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.13 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.31 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.3 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.21 |
kasA | 2518144 | c.29dupG | frameshift_variant | 0.17 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.2 |
eis | 2714366 | p.Val323Leu | missense_variant | 0.2 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.21 |
ahpC | 2726756 | c.564C>G | synonymous_variant | 0.35 |
pepQ | 2859381 | c.1038C>G | synonymous_variant | 0.18 |
ribD | 2987307 | p.Ala157Pro | missense_variant | 0.3 |
Rv2752c | 3064552 | p.Arg547Pro | missense_variant | 0.23 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.28 |
Rv2752c | 3064741 | p.Gly484Ala | missense_variant | 0.4 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.46 |
thyA | 3074654 | c.-183T>G | upstream_gene_variant | 0.5 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.86 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.17 |
Rv3083 | 3448929 | p.Tyr142* | stop_gained | 0.24 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474601 | p.Arg199Gly | missense_variant | 0.17 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.11 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.33 |
fbiB | 3642734 | c.1200G>C | synonymous_variant | 0.4 |
fbiB | 3642772 | p.Asp413Ala | missense_variant | 0.33 |
alr | 3840719 | c.702A>G | synonymous_variant | 0.52 |
rpoA | 3878238 | p.Asp90Glu | missense_variant | 0.15 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.63 |
clpC1 | 4039363 | p.Ala448Pro | missense_variant | 0.4 |
clpC1 | 4039932 | p.Gly258Val | missense_variant | 0.18 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.24 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.22 |
embC | 4241429 | p.Phe523Val | missense_variant | 0.71 |
embC | 4242425 | p.Arg855Gly | missense_variant | 0.29 |
embC | 4242476 | p.Pro872Ala | missense_variant | 0.2 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242822 | p.Val987Gly | missense_variant | 0.23 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.23 |
embA | 4244263 | p.Leu344Arg | missense_variant | 0.22 |
embA | 4245025 | p.His598Arg | missense_variant | 0.12 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.18 |
embB | 4247603 | p.Leu364Val | missense_variant | 0.31 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.2 |
embB | 4249732 | c.3219C>G | synonymous_variant | 0.12 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.29 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.38 |
ethA | 4327672 | c.-199G>A | upstream_gene_variant | 0.29 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 0.29 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.36 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.18 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.17 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.64 |