TB-Profiler result

Run: ERR4831741
Summary

Run ID: ERR4831741

Sample name:

Date: 01-04-2023 21:05:37

Number of reads: 1209021

Percentage reads mapped: 95.74

Strain: lineage1.1.1

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
lineage1 Indo-Oceanic EAI RD239 0.95
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.96
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.95
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 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289202 p.Cys14Arg missense_variant 0.88 pyrazinamide
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 0.91
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7433 c.132G>A synonymous_variant 0.15
gyrA 7543 p.Met81Thr missense_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.93
gyrA 8832 p.Ile511Val missense_variant 0.11
gyrA 9143 c.1842T>C synonymous_variant 0.91
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620045 p.Gly52Val missense_variant 0.15
rpoB 762689 p.Gln961His missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.93
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 777377 c.1104C>A synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781694 c.135G>A synonymous_variant 0.91
rplC 801270 c.462T>C synonymous_variant 0.11
fbiC 1304007 c.1077G>T synonymous_variant 0.13
Rv1258c 1406949 p.Ala131Asp missense_variant 0.22
Rv1258c 1407466 c.-126G>T upstream_gene_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472484 n.639A>G non_coding_transcript_exon_variant 0.2
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.16
rrs 1472766 n.921G>C non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.1
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.1
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473342 n.1497G>T non_coding_transcript_exon_variant 0.14
rrl 1473748 n.91A>G non_coding_transcript_exon_variant 0.18
rrl 1474130 n.473C>A non_coding_transcript_exon_variant 0.14
rrl 1474164 n.507C>A non_coding_transcript_exon_variant 0.15
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rrl 1474944 n.1287G>T non_coding_transcript_exon_variant 0.2
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.25
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.25
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.27
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.25
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.27
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.2
rrl 1476290 n.2633C>A non_coding_transcript_exon_variant 0.18
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.18
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.18
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.18
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.22
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.22
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.22
inhA 1674484 p.Ile95Val missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.12
rpsA 1834319 p.Val260Ile missense_variant 0.81
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918199 p.Leu87Pro missense_variant 0.13
ndh 2103159 c.-118delC upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155321 p.Ala264Glu missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.96
PPE35 2168214 p.Thr800Met missense_variant 0.25
PPE35 2170557 p.Ala19Glu missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 0.97
Rv1979c 2223144 p.Arg7Ser missense_variant 0.88
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289437 c.-196A>G upstream_gene_variant 0.11
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518725 p.Ala204Glu missense_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 0.97
ahpC 2726650 p.Ser153Leu missense_variant 0.12
ahpC 2726763 p.Leu191Phe missense_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 0.91
Rv2752c 3065311 p.Thr294Lys missense_variant 0.13
thyX 3067476 p.Gln157Arg missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339639 c.522C>A synonymous_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 0.94
Rv3083 3449057 p.Ser185Asn missense_variant 0.15
Rv3083 3449094 c.591C>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474172 p.Asp56His missense_variant 0.11
fprA 3474597 c.591C>A synonymous_variant 0.97
fprA 3474914 p.Ala303Val missense_variant 0.12
fprA 3474929 p.Gly308Val missense_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 0.85
Rv3236c 3612021 p.Gly366Cys missense_variant 0.13
clpC1 4038170 c.2535G>T synonymous_variant 0.14
clpC1 4038908 c.1797C>G synonymous_variant 0.12
clpC1 4038923 c.1782A>T synonymous_variant 0.12
clpC1 4038932 c.1773G>C synonymous_variant 0.11
clpC1 4039616 c.1089G>C synonymous_variant 0.14
clpC1 4040198 p.Leu169Phe missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.95
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241642 p.Ala594Ser missense_variant 0.14
embA 4242358 c.-875C>A upstream_gene_variant 0.15
embC 4242557 p.Gln899Glu missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242707 p.Asp949Tyr missense_variant 0.17
embA 4243848 p.Val206Met missense_variant 1.0
embA 4243877 c.645G>T synonymous_variant 0.17
embA 4244096 c.864C>T synonymous_variant 0.93
embA 4244190 p.Ala320Thr missense_variant 0.13
embA 4245461 c.2229C>A synonymous_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246732 c.219G>T synonymous_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 0.92
embB 4249485 p.Gly991Asp missense_variant 0.14
aftB 4268903 c.-67A>G upstream_gene_variant 0.12
aftB 4268943 c.-107C>A upstream_gene_variant 0.13
ubiA 4269350 p.Ile162Leu missense_variant 0.93
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 0.94
ethA 4326926 p.Ser183Ile missense_variant 0.15
ethA 4327554 c.-81G>C upstream_gene_variant 0.1
ethA 4328145 c.-672C>T upstream_gene_variant 0.94
whiB6 4338242 p.Gln94Glu missense_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.97
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407703 p.Ala167Asp missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0