Run ID: ERR4872269
Sample name:
Date: 01-04-2023 21:29:58
Number of reads: 1048526
Percentage reads mapped: 26.05
Strain: lineage2.2.1
Drug-resistance: XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rplC | 801268 | p.Cys154Arg | missense_variant | 1.0 | linezolid |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.98 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288928 | p.Gly105Val | missense_variant | 1.0 | pyrazinamide |
embB | 4247399 | p.Asn296His | missense_variant | 1.0 | ethambutol |
ethA | 4327363 | c.110delA | frameshift_variant | 1.0 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 762863 | c.-507T>C | upstream_gene_variant | 0.21 |
rpoB | 762872 | p.Met1022Ile | missense_variant | 0.25 |
rpoB | 762878 | p.Ile1024Met | missense_variant | 0.26 |
rpoB | 762879 | p.Met1025Leu | missense_variant | 0.26 |
rpoC | 762899 | c.-471G>C | upstream_gene_variant | 0.41 |
rpoB | 762925 | p.Thr1040Ile | missense_variant | 0.46 |
rpoC | 762929 | c.-441G>C | upstream_gene_variant | 0.46 |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.45 |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.45 |
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.41 |
rpoC | 762980 | c.-390T>C | upstream_gene_variant | 0.41 |
rpoC | 762983 | c.-387C>T | upstream_gene_variant | 0.4 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.41 |
rpoC | 762998 | c.-372G>A | upstream_gene_variant | 0.4 |
rpoB | 763005 | p.Cys1067Val | missense_variant | 0.31 |
rpoB | 763014 | p.Met1070Leu | missense_variant | 0.27 |
rpoB | 763017 | p.Gln1071Glu | missense_variant | 0.27 |
rpoC | 763028 | c.-342T>C | upstream_gene_variant | 0.26 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764348 | p.Met327Leu | missense_variant | 0.18 |
rpoC | 764355 | p.Gln329Pro | missense_variant | 0.28 |
rpoC | 764359 | c.990C>G | synonymous_variant | 0.28 |
rpoC | 764371 | c.1002G>C | synonymous_variant | 0.15 |
rpoC | 764374 | c.1005C>T | synonymous_variant | 0.17 |
rpoC | 764377 | c.1008C>G | synonymous_variant | 0.17 |
rpoC | 764383 | c.1014C>G | synonymous_variant | 0.2 |
rpoC | 764387 | c.1018T>C | synonymous_variant | 0.23 |
rpoC | 764401 | c.1032C>T | synonymous_variant | 0.26 |
rpoC | 764405 | c.1036_1038delAGGinsCGC | synonymous_variant | 0.28 |
rpoC | 764410 | c.1041G>C | synonymous_variant | 0.29 |
rpoC | 764428 | c.1059G>C | synonymous_variant | 0.29 |
rpoC | 764434 | c.1065A>G | synonymous_variant | 0.28 |
rpoC | 764435 | c.1066_1068delAGGinsCGC | synonymous_variant | 0.29 |
rpoC | 764443 | p.Ile358Met | missense_variant | 0.27 |
rpoC | 764446 | p.Asp359Glu | missense_variant | 0.26 |
rpoC | 764450 | p.Gly361Arg | missense_variant | 0.27 |
rpoC | 764461 | p.Glu364Asp | missense_variant | 0.27 |
rpoC | 764468 | p.Val367Ile | missense_variant | 0.28 |
rpoC | 764471 | p.Asn368Arg | missense_variant | 0.27 |
rpoC | 764479 | c.1110G>A | synonymous_variant | 0.28 |
rpoC | 764500 | c.1131C>G | synonymous_variant | 0.23 |
rpoC | 764503 | c.1134G>C | synonymous_variant | 0.21 |
rpoC | 764509 | c.1140G>C | synonymous_variant | 0.21 |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.22 |
rpoC | 764527 | c.1158C>T | synonymous_variant | 0.21 |
rpoC | 764582 | p.Leu405Met | missense_variant | 0.13 |
rpoC | 764587 | c.1218C>G | synonymous_variant | 0.19 |
rpoC | 764605 | c.1236G>C | synonymous_variant | 0.35 |
rpoC | 764611 | c.1242G>C | synonymous_variant | 0.34 |
rpoC | 764623 | c.1254C>G | synonymous_variant | 0.33 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.33 |
rpoC | 764641 | c.1272C>T | synonymous_variant | 0.3 |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.3 |
rpoC | 764660 | p.Val431Thr | missense_variant | 0.3 |
rpoC | 764665 | c.1296C>G | synonymous_variant | 0.31 |
rpoC | 764668 | c.1299C>A | synonymous_variant | 0.28 |
rpoC | 764672 | p.Gln435Glu | missense_variant | 0.28 |
rpoC | 764677 | c.1308C>G | synonymous_variant | 0.27 |
rpoC | 764687 | p.Gln440Glu | missense_variant | 0.26 |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.28 |
rpoC | 764705 | p.Leu446Lys | missense_variant | 0.27 |
rpoC | 764840 | p.Ile491Val | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpR5 | 779161 | p.Thr58Pro | missense_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472349 | n.504A>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472374 | n.529T>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472379 | n.534T>G | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472382 | n.537G>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472390 | n.545T>C | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472812 | n.967A>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476266 | n.2609G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476279 | n.2622G>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476301 | n.2644A>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.53 |
rrl | 1476339 | n.2682G>A | non_coding_transcript_exon_variant | 0.57 |
rrl | 1476356 | n.2699C>T | non_coding_transcript_exon_variant | 0.64 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.64 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476384 | n.2727G>A | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.77 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.77 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.76 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.76 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476501 | n.2844C>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.66 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.61 |
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476521 | n.2864C>T | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476524 | n.2867C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476525 | n.2868A>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476529 | n.2872A>G | non_coding_transcript_exon_variant | 0.49 |
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.48 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.48 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.47 |
rrl | 1476540 | n.2883C>T | non_coding_transcript_exon_variant | 0.47 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476572 | n.2915G>A | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476573 | n.2916A>T | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476584 | n.2927C>G | non_coding_transcript_exon_variant | 0.25 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714919 | p.His138Gln | missense_variant | 0.13 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.25 |
Rv2752c | 3066058 | p.Cys45Phe | missense_variant | 1.0 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.75 |
fbiD | 3339746 | p.Ala210Gly | missense_variant | 0.5 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474213 | p.Lys69Asn | missense_variant | 0.16 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
rpoA | 3878590 | c.-83G>C | upstream_gene_variant | 0.18 |
rpoA | 3878597 | c.-90G>C | upstream_gene_variant | 0.2 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.56 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4248324 | p.Ala604Gly | missense_variant | 0.22 |
embB | 4248328 | c.1815G>C | synonymous_variant | 0.16 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |