TB-Profiler result

Run: ERR4872269
Summary

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

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
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
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
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
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
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