TB-Profiler result

Run: ERR221563
Summary

Run ID: ERR221563

Sample name:

Date: 31-03-2023 16:16:37

Number of reads: 3132471

Percentage reads mapped: 90.65

Strain: lineage1.1.3.2

Drug-resistance: Sensitive

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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 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.2 Indo-Oceanic NA RD239 0.99
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
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 5075 c.-165_-164insG upstream_gene_variant 1.0
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 8188 p.Leu296Pro missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
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 619695 c.-196G>A upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 1.0
Rv1258c 1406807 c.534G>A synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.1
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.11
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.16
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.32
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.32
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.31
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.32
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.25
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.21
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.12
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.12
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.12
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.15
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.15
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.15
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.32
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.23
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.22
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.22
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.22
rrs 1473262 n.1417T>A non_coding_transcript_exon_variant 0.22
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.16
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.15
rrl 1474187 n.530T>C non_coding_transcript_exon_variant 0.15
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.13
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.14
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.14
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.17
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.12
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.15
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.16
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.16
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.17
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.17
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.17
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.16
rrl 1475869 n.2212C>T non_coding_transcript_exon_variant 0.15
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.15
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.24
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.25
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.21
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.22
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.21
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.21
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.21
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.28
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.27
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.27
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.37
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.38
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.37
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.36
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.35
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.47
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.47
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.53
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.55
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.57
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.55
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.45
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.45
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.38
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22
inhA 1674883 p.Ile228Val missense_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
PPE35 2167983 p.Gly877Asp 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
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99
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
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
fbiB 3642173 c.639G>A synonymous_variant 1.0
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.3
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.27
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
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_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 0.99
gid 4407873 c.330G>T synonymous_variant 1.0