TB-Profiler result

Run: ERR4817751
Summary

Run ID: ERR4817751

Sample name:

Date: 01-04-2023 15:10:40

Number of reads: 4652570

Percentage reads mapped: 96.16

Strain: lineage1.1.3.3

Drug-resistance: Other

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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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.3 Indo-Oceanic NA RD239 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.31 streptomycin
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
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8403 p.His368Tyr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.99
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620616 p.Phe242Leu missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776006 c.2475C>T synonymous_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776826 p.Glu552Gly missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781486 c.-74C>G upstream_gene_variant 0.52
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.16
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.15
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.2
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.13
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.18
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.11
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.16
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.18
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.46
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.5
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.45
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.53
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.5
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.16
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.18
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.3
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.3
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.3
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.16
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.24
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.19
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.15
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.14
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.16
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.26
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.22
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.26
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 0.19
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.12
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.16
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.11
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.11
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.11
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.14
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.11
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.12
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.39
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.41
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.52
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.48
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.52
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.45
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.17
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.19
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.15
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.16
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.17
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.31
rrl 1474706 n.1049G>A non_coding_transcript_exon_variant 0.19
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.19
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.24
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.38
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.45
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.45
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.31
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.2
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.35
rrl 1475031 n.1374G>C non_coding_transcript_exon_variant 0.2
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.12
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.15
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.18
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.11
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.13
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.18
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.21
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
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168124 p.Gly830Glu missense_variant 1.0
PPE35 2169630 p.Asn328Ser missense_variant 1.0
PPE35 2169757 p.Asn286Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519100 p.Ala329Val missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747666 c.-68A>G upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449709 c.1206C>G synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3840493 c.928C>T synonymous_variant 1.0
alr 3841349 c.72C>A synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240207 c.345G>A synonymous_variant 0.99
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267431 p.Ser469Leu missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338208 p.Pro105Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0