TB-Profiler result

Run: ERR1665402
Summary

Run ID: ERR1665402

Sample name:

Date: 31-03-2023 14:55:20

Number of reads: 4988378

Percentage reads mapped: 92.09

Strain: lineage2.2.1

Drug-resistance: MDR-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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.6 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.89 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2288902 p.Thr114Pro missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4326964 c.509delA 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
rpoB 762285 p.Arg827Cys missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_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
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 1472517 n.672T>A non_coding_transcript_exon_variant 0.21
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.31
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.4
rrs 1472548 n.703A>G non_coding_transcript_exon_variant 0.11
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.51
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.56
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.59
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.6
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.71
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.71
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.75
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.74
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.69
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.69
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.64
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.68
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.62
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.62
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.65
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.65
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.61
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.64
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.66
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.64
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.62
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.61
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.45
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.35
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.19
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.14
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.14
rrs 1472858 n.1013_1014insA non_coding_transcript_exon_variant 0.12
rrs 1472861 n.1016G>T non_coding_transcript_exon_variant 0.12
rrs 1472863 n.1018T>C non_coding_transcript_exon_variant 0.12
rrs 1472873 n.1028C>G non_coding_transcript_exon_variant 0.12
rrs 1472875 n.1030T>A non_coding_transcript_exon_variant 0.12
rrs 1472876 n.1031G>A non_coding_transcript_exon_variant 0.11
rrs 1472877 n.1032T>A non_coding_transcript_exon_variant 0.11
rrs 1472880 n.1035_1036insA non_coding_transcript_exon_variant 0.16
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.19
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.11
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.13
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.11
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.11
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.1
rrs 1473281 n.1436C>G non_coding_transcript_exon_variant 0.1
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.1
rrs 1473297 n.1452G>C non_coding_transcript_exon_variant 0.1
rrs 1473303 n.1458T>C non_coding_transcript_exon_variant 0.1
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 0.13
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.13
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.13
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.13
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.13
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.15
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.1
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.15
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.15
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.19
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.23
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.34
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.4
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.32
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.29
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.33
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.3
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.33
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.29
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.31
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.29
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.31
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.35
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.32
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.4
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.39
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.42
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.41
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.41
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.46
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.46
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.49
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.49
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.49
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.3
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.25
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.24
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.23
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.23
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.24
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.22
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.23
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.23
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.23
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.24
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.22
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 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
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
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