TB-Profiler result

Run: ERR4863405
Summary

Run ID: ERR4863405

Sample name:

Date: 01-04-2023 21:32:03

Number of reads: 4449346

Percentage reads mapped: 45.57

Strain: lineage4.1.2.1;lineage2.2.1

Drug-resistance: Pre-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 0.7
lineage4 Euro-American LAM;T;S;X;H None 0.31
lineage4.1 Euro-American T;X;H None 0.25
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.64
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.68
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.33
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.Asp94Gly missense_variant 0.54 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.65 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.64 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.49 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.15 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.6 isoniazid
embB 4247429 p.Met306Val missense_variant 0.72 ethambutol
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 491591 p.Lys270Met missense_variant 0.37
fgd1 491742 c.960T>C synonymous_variant 0.63
mshA 575679 p.Asn111Ser missense_variant 0.44
mshA 575907 p.Ala187Val missense_variant 0.78
mshA 576108 p.Ala254Gly missense_variant 0.4
mshA 576482 p.Val379Leu missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 0.61
rpoB 760115 c.309C>T synonymous_variant 0.31
rpoB 760324 p.Leu173Pro missense_variant 0.64
rpoC 763031 c.-339T>C upstream_gene_variant 0.57
rpoC 765150 p.Gly594Glu missense_variant 0.4
rpoC 766645 p.Glu1092Asp missense_variant 0.71
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.76
mmpL5 776182 p.Asp767Asn missense_variant 0.7
mmpL5 778292 c.188dupC frameshift_variant 0.57
mmpR5 779243 p.Val85Gly missense_variant 0.67
mmpS5 779615 c.-710C>G upstream_gene_variant 0.62
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.77
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.11
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.2
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.21
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.26
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.31
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.32
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.4
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.41
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.42
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.42
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.46
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.45
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.44
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.43
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.53
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.48
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.48
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.54
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.56
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.47
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.46
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.38
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.37
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.3
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.31
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.42
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.26
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.49
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.5
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.46
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.25
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.21
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.2
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.11
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.13
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.15
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.13
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.16
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.13
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.19
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.1
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.15
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.14
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.2
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.17
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.13
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.13
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.12
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.13
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.11
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.1
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.1
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.11
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.13
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.13
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.12
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.12
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.14
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.13
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.13
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.13
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.12
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.18
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.23
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.21
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.29
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.21
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.2
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.29
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.3
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.22
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.19
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.2
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.18
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.19
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.21
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.35
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.32
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.35
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.49
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.52
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.59
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.56
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.52
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.55
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.55
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.53
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.52
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.53
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.5
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.55
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.55
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.55
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.65
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.69
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.73
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.75
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.75
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.76
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.69
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.69
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.64
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.69
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.69
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.62
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.47
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.27
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.22
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.15
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.22
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.22
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.14
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.13
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
rpsA 1834177 c.636A>C synonymous_variant 0.78
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.69
PPE35 2167926 p.Leu896Ser missense_variant 0.65
PPE35 2170048 p.Leu189Val missense_variant 0.35
PPE35 2170053 p.Thr187Ser missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288944 p.Thr100Pro missense_variant 0.65
kasA 2518076 c.-39C>T upstream_gene_variant 0.26
eis 2715368 c.-54_-37delGTCGTCGTAATATTCACG upstream_gene_variant 0.64
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.53
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.19
embA 4243460 c.228C>T synonymous_variant 0.73
embB 4246544 p.Thr11Pro missense_variant 0.37
embB 4246548 p.Pro12Gln missense_variant 0.26
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246563 p.Leu17Trp missense_variant 0.31
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4246584 p.Arg24Pro missense_variant 0.18
embB 4247050 c.537C>T synonymous_variant 0.31
aftB 4267647 p.Asp397Gly missense_variant 0.79
ethA 4326623 p.Pro284Leu missense_variant 0.54
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.51
gid 4407927 p.Glu92Asp missense_variant 0.64