TB-Profiler result

Run: ERR4819703

Summary

Run ID: ERR4819703

Sample name:

Date: 01-04-2023 16:15:28

Number of reads: 38264

Percentage reads mapped: 93.29

Strain: lineage4.9

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 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 5183 c.-57G>A upstream_gene_variant 0.25
gyrB 5193 c.-47G>A upstream_gene_variant 0.33
gyrB 6232 c.993C>T synonymous_variant 1.0
gyrB 6279 p.Gly347Asp missense_variant 0.5
gyrB 6455 p.Val406Ile missense_variant 1.0
gyrB 6467 p.Ala410Thr missense_variant 1.0
gyrB 7133 p.Val632Met missense_variant 1.0
gyrA 7773 p.Gly158Ser missense_variant 0.33
gyrA 8558 c.1257C>T synonymous_variant 1.0
gyrA 8947 p.Leu549* stop_gained 1.0
gyrA 9759 p.Glu820Lys missense_variant 0.5
fgd1 490729 c.-54C>T upstream_gene_variant 1.0
fgd1 490742 c.-41C>T upstream_gene_variant 1.0
fgd1 490819 p.Glu13Lys missense_variant 0.25
mshA 575763 p.Ala139Val missense_variant 1.0
ccsA 619694 c.-197C>T upstream_gene_variant 0.5
ccsA 620730 c.840C>T synonymous_variant 1.0
rpoB 760805 c.999G>A synonymous_variant 1.0
rpoB 760806 p.Ala334Thr missense_variant 1.0
rpoB 761415 p.Gln537* stop_gained 1.0
rpoB 761441 c.1635C>T synonymous_variant 1.0
rpoB 761531 c.1725C>T synonymous_variant 1.0
rpoB 761538 p.Arg578Cys missense_variant 1.0
rpoB 761752 p.Ala649Val missense_variant 1.0
rpoB 762510 p.Ala902Thr missense_variant 0.4
rpoC 762524 c.-846G>A upstream_gene_variant 0.5
rpoB 762928 p.Gly1041Glu missense_variant 1.0
rpoB 763300 p.Ser1165Phe missense_variant 1.0
rpoC 764941 c.1572G>A synonymous_variant 1.0
rpoC 766367 p.Ala1000Ser missense_variant 0.5
rpoC 766389 p.Gly1007Asp missense_variant 1.0
rpoC 766756 c.3387G>A synonymous_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776042 c.2439C>T synonymous_variant 1.0
mmpL5 776075 c.2406C>T synonymous_variant 1.0
mmpL5 776095 p.Arg796Cys missense_variant 1.0
mmpL5 776097 p.Thr795Ile missense_variant 1.0
mmpL5 776433 p.Ser683Leu missense_variant 1.0
mmpL5 776436 p.Ala682Val missense_variant 1.0
mmpL5 777876 p.Arg202His missense_variant 0.5
mmpL5 777909 p.Ala191Val missense_variant 0.5
mmpL5 777915 p.Ser189Leu missense_variant 0.5
mmpL5 777919 p.Gly188Ser missense_variant 1.0
mmpL5 778017 p.Gly155Asp missense_variant 1.0
mmpR5 779455 p.Arg156* stop_gained 1.0
rpsL 781645 p.Gln29Arg missense_variant 0.5
rplC 800953 p.Ala49Thr missense_variant 1.0
rplC 801415 p.Gly203Ser missense_variant 0.5
rplC 801418 p.Gly204Arg missense_variant 0.5
fbiC 1302760 c.-171C>T upstream_gene_variant 1.0
fbiC 1305074 p.Ser715Asn missense_variant 0.5
embR 1417140 p.Ala70Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471662 n.-184C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472214 n.369C>T non_coding_transcript_exon_variant 0.5
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.67
rrs 1472648 n.803G>A non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.25
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.25
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.25
rrs 1472669 n.827delG non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.5
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.5
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrl 1473968 n.311C>T non_coding_transcript_exon_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.2
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.2
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 0.29
rrl 1474290 n.633T>C non_coding_transcript_exon_variant 1.0
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 1.0
rrl 1474846 n.1189T>C non_coding_transcript_exon_variant 0.4
rrl 1474941 n.1284G>A non_coding_transcript_exon_variant 1.0
rrl 1475109 n.1452C>T non_coding_transcript_exon_variant 0.5
rrl 1475754 n.2097G>A non_coding_transcript_exon_variant 1.0
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.2
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.2
rrl 1475940 n.2283C>T non_coding_transcript_exon_variant 1.0
rrl 1476121 n.2464C>T non_coding_transcript_exon_variant 0.33
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.5
rrl 1476643 n.2986A>G non_coding_transcript_exon_variant 1.0
rrl 1476777 n.3120C>T non_coding_transcript_exon_variant 0.2
inhA 1674584 p.Ala128Val missense_variant 1.0
rpsA 1834799 p.Glu420Lys missense_variant 1.0
rpsA 1834809 p.Arg423His missense_variant 1.0
ndh 2101828 c.1215C>T synonymous_variant 0.5
katG 2154466 p.Cys549Tyr missense_variant 1.0
katG 2154470 p.Gly548Ser missense_variant 1.0
katG 2154491 p.Ala541Thr missense_variant 1.0
katG 2155533 c.579C>T synonymous_variant 1.0
katG 2155554 c.558C>T synonymous_variant 1.0
katG 2155563 c.549C>T synonymous_variant 1.0
katG 2155933 p.Ala60Val missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168838 p.Pro592Leu missense_variant 0.5
PPE35 2170280 c.333C>G synonymous_variant 1.0
PPE35 2170776 c.-164T>C upstream_gene_variant 0.25
Rv1979c 2222451 c.714C>T synonymous_variant 1.0
Rv1979c 2222902 p.Arg88His missense_variant 1.0
Rv1979c 2222915 p.Ala84Thr missense_variant 1.0
Rv1979c 2222927 p.Ala80Thr missense_variant 1.0
kasA 2517935 c.-180C>T upstream_gene_variant 1.0
kasA 2517986 c.-129C>T upstream_gene_variant 0.5
kasA 2518093 c.-22C>T upstream_gene_variant 1.0
kasA 2518143 p.Gly10Asp missense_variant 1.0
kasA 2518434 p.Arg107Gln missense_variant 0.5
kasA 2518458 p.Gly115Asp missense_variant 1.0
kasA 2519122 c.1008G>A synonymous_variant 1.0
ahpC 2726562 p.Val124Ile missense_variant 1.0
folC 2747324 p.Arg92His missense_variant 1.0
pepQ 2859415 p.Gly335Asp missense_variant 1.0
pepQ 2859735 c.684G>T synonymous_variant 1.0
pepQ 2860440 c.-22G>A upstream_gene_variant 1.0
ribD 2986794 c.-45G>A upstream_gene_variant 1.0
ribD 2986799 c.-40G>A upstream_gene_variant 1.0
ribD 2986814 c.-25G>A upstream_gene_variant 0.5
Rv2752c 3065027 p.Arg389Trp missense_variant 1.0
Rv2752c 3065300 p.Asp298Asn missense_variant 1.0
Rv2752c 3065304 c.888G>A synonymous_variant 1.0
Rv2752c 3065315 p.Glu293Lys missense_variant 1.0
Rv2752c 3065341 p.Ser284Phe missense_variant 1.0
Rv2752c 3065592 c.600G>A synonymous_variant 1.0
Rv2752c 3065833 p.Arg120His missense_variant 1.0
thyA 3073788 c.684G>A synonymous_variant 0.5
fprA 3475183 p.Ala393Thr missense_variant 1.0
whiB7 3568824 c.-145A>G upstream_gene_variant 1.0
Rv3236c 3612298 c.819C>A synonymous_variant 1.0
fbiB 3641558 c.24C>T synonymous_variant 0.5
fbiB 3641563 p.Ser10Leu missense_variant 0.5
fbiB 3641592 c.58C>T synonymous_variant 1.0
fbiB 3642008 c.474C>T synonymous_variant 1.0
fbiB 3642011 c.477C>T synonymous_variant 0.5
fbiB 3642016 p.Thr161Ile missense_variant 0.5
fbiB 3642039 p.Gly169Ser missense_variant 0.5
fbiB 3642045 p.Ala171Thr missense_variant 0.5
fbiB 3642055 p.Arg174His missense_variant 0.5
alr 3840533 c.888G>A synonymous_variant 0.5
alr 3841219 p.Asp68Asn missense_variant 1.0
alr 3841449 c.-29C>T upstream_gene_variant 1.0
alr 3841455 c.-35C>T upstream_gene_variant 1.0
alr 3841461 c.-41C>T upstream_gene_variant 1.0
rpoA 3877795 p.Pro238Leu missense_variant 0.5
rpoA 3877806 c.702C>T synonymous_variant 0.5
clpC1 4039761 p.Gly315Asp missense_variant 1.0
clpC1 4039792 p.Ala305Thr missense_variant 1.0
clpC1 4039812 p.Ala298Val missense_variant 1.0
clpC1 4039814 c.891C>T synonymous_variant 1.0
clpC1 4040109 p.Arg199Gln missense_variant 1.0
clpC1 4040183 c.522C>T synonymous_variant 1.0
embC 4240745 p.Gly295Ser missense_variant 1.0
embA 4243619 c.387C>T synonymous_variant 1.0
embA 4243627 p.Ala132Val missense_variant 1.0
embA 4243666 p.Thr145Ile missense_variant 0.5
embA 4244672 c.1440C>T synonymous_variant 0.5
embA 4246429 p.Ala1066Val missense_variant 1.0
embB 4246922 p.Arg137Cys missense_variant 1.0
embB 4247087 c.574C>T synonymous_variant 1.0
embB 4247092 c.579C>T synonymous_variant 1.0
embB 4247103 p.Pro197Leu missense_variant 1.0
embB 4247107 c.594C>T synonymous_variant 1.0
embB 4247121 p.Ser203Leu missense_variant 1.0
embB 4247628 p.Arg372His missense_variant 1.0
embB 4248904 c.2391G>A synonymous_variant 1.0
aftB 4267391 c.1446G>A synonymous_variant 1.0
aftB 4267421 c.1416C>T synonymous_variant 1.0
aftB 4267828 p.Arg337Trp missense_variant 1.0
aftB 4268356 p.Pro161Ser missense_variant 0.5
ubiA 4269214 p.Arg207His missense_variant 0.5
ubiA 4269217 p.Ile206Thr missense_variant 0.5
ethA 4327762 c.-289G>A upstream_gene_variant 1.0
whiB6 4338417 c.105G>A synonymous_variant 0.67
gid 4408301 c.-99G>A upstream_gene_variant 1.0
gid 4408304 c.-102G>A upstream_gene_variant 1.0