TB-Profiler result

Run: ERR4820264
Summary

Run ID: ERR4820264

Sample name:

Date: 01-04-2023 16:35:02

Number of reads: 2194926

Percentage reads mapped: 61.48

Strain: lineage1.1.2

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
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.56 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.93 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
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr 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 491494 p.Asp238Asn missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760490 c.684C>T synonymous_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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpR5 779474 p.Gly162Glu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303442 p.Leu171Trp missense_variant 1.0
fbiC 1304855 p.Val642Ala missense_variant 0.43
fbiC 1304860 p.Lys644Glu missense_variant 0.18
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472160 n.315C>A non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472181 n.336G>T non_coding_transcript_exon_variant 0.18
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.18
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.14
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.14
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.13
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.13
rrs 1472243 n.398G>A non_coding_transcript_exon_variant 0.13
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.14
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.87
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.87
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.9
rrs 1472573 n.728C>G non_coding_transcript_exon_variant 0.85
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.86
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.86
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.8
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.8
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.77
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.74
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.43
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.56
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.6
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.9
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.47
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.9
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.95
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.95
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.93
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.92
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.9
rrs 1472806 n.961A>T non_coding_transcript_exon_variant 0.23
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.58
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.29
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.33
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.25
rrs 1472896 n.1051T>C non_coding_transcript_exon_variant 0.25
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.17
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.21
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.46
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.57
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.57
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.58
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.58
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.56
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.54
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.54
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.47
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.37
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.29
rrl 1474124 n.467G>A non_coding_transcript_exon_variant 0.29
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.67
rrl 1474236 n.579G>A non_coding_transcript_exon_variant 0.8
rrl 1474249 n.592G>C non_coding_transcript_exon_variant 0.8
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.8
rrl 1474276 n.619C>T non_coding_transcript_exon_variant 0.5
rrl 1476009 n.2352G>T non_coding_transcript_exon_variant 0.12
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.21
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.11
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101850 p.Val398Ala missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155402 p.Gly237Ala missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.14
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 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 3448768 p.Ala89Thr 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
fbiA 3640852 p.Leu104Phe missense_variant 1.0
fbiB 3641882 c.348C>A synonymous_variant 1.0
rpoA 3878268 c.240C>T synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040814 c.-110G>A upstream_gene_variant 1.0
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
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 4407873 c.330G>T synonymous_variant 1.0