TB-Profiler result

Run: ERR4407539
Summary

Run ID: ERR4407539

Sample name:

Date: 01-04-2023 05:49:11

Number of reads: 502183

Percentage reads mapped: 96.2

Strain: lineage4.1.2.1

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
embA 4243221 c.-12C>T upstream_gene_variant 0.11 ethambutol
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 7016 p.Ala593Ser missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7554 p.His85Asn missense_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8095 p.Gly265Asp missense_variant 0.15
gyrA 8415 p.Val372Ile missense_variant 0.22
gyrA 8828 c.1527T>C synonymous_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490886 p.Ala35Val missense_variant 0.22
fgd1 490947 c.165G>A synonymous_variant 0.22
fgd1 491358 p.Phe192Leu missense_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491715 c.933C>T synonymous_variant 0.15
mshA 575515 c.168G>A synonymous_variant 0.15
mshA 575560 p.Tyr71* stop_gained 0.14
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620477 p.Phe196Ser missense_variant 0.17
ccsA 620532 c.642T>G synonymous_variant 0.22
rpoB 759790 c.-17T>C upstream_gene_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760918 p.Arg371His missense_variant 0.14
rpoB 761193 p.Gly463Arg missense_variant 0.22
rpoB 761302 p.Arg499Gln missense_variant 0.15
rpoB 761698 p.Asp631Ala missense_variant 0.12
rpoB 761820 p.Ser672Pro missense_variant 0.17
rpoB 761838 p.Ala678Thr missense_variant 0.13
rpoB 761887 p.Gln694Arg missense_variant 0.12
rpoB 761892 p.Ile696Phe missense_variant 0.12
rpoC 763810 p.Glu147Asp missense_variant 0.13
rpoC 764246 p.Leu293Phe missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765154 p.Asp595Glu missense_variant 0.12
rpoC 767036 p.Ala1223Thr missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776249 c.2232A>G synonymous_variant 0.1
mmpL5 776742 p.Pro580Arg missense_variant 1.0
mmpL5 777164 c.1317C>T synonymous_variant 0.13
mmpL5 777173 c.1308C>T synonymous_variant 0.14
mmpL5 777176 p.Glu435Asp missense_variant 0.12
mmpL5 777903 p.Val193Ala missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781548 c.-12G>T upstream_gene_variant 0.15
fbiC 1303471 p.Val181Met missense_variant 0.29
fbiC 1303526 p.Ser199Leu missense_variant 0.2
fbiC 1304973 c.2043C>A synonymous_variant 0.12
fbiC 1305319 p.Gln797Lys missense_variant 0.17
Rv1258c 1406405 c.936G>T synonymous_variant 0.12
Rv1258c 1407150 p.Thr64Ile missense_variant 0.18
embR 1416843 p.Asp169Asn missense_variant 0.11
embR 1417473 c.-126G>C upstream_gene_variant 0.22
atpE 1461199 p.Pro52Arg missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472238 n.393G>C non_coding_transcript_exon_variant 0.29
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.33
rrs 1472837 n.992C>G non_coding_transcript_exon_variant 0.25
rrs 1472838 n.993_994insT non_coding_transcript_exon_variant 0.25
rrs 1472843 n.999_1001delCGC non_coding_transcript_exon_variant 0.25
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.29
rrs 1472860 n.1015C>T non_coding_transcript_exon_variant 0.29
rrs 1472861 n.1016G>A non_coding_transcript_exon_variant 0.29
rrs 1472863 n.1018T>G non_coding_transcript_exon_variant 0.29
rrs 1472865 n.1020_1021insT non_coding_transcript_exon_variant 0.33
rrs 1472869 n.1024G>T non_coding_transcript_exon_variant 0.33
rrs 1472873 n.1028C>G non_coding_transcript_exon_variant 0.33
rrs 1472874 n.1029C>G non_coding_transcript_exon_variant 0.33
rrs 1472875 n.1030_1031insTG non_coding_transcript_exon_variant 0.4
rrs 1472878 n.1033G>T non_coding_transcript_exon_variant 0.4
rrs 1472879 n.1034T>C non_coding_transcript_exon_variant 0.33
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.33
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.33
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.33
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.33
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.33
rrl 1475255 n.1598C>T non_coding_transcript_exon_variant 0.13
rpsA 1834010 c.469C>A synonymous_variant 0.11
rpsA 1834031 p.Tyr164His missense_variant 0.12
ndh 2102126 p.Leu306Arg missense_variant 0.12
katG 2153933 p.Ala727Ser missense_variant 0.18
katG 2155101 c.1011C>T synonymous_variant 0.25
katG 2155957 p.Pro52Gln missense_variant 0.2
PPE35 2169110 p.Phe501Leu missense_variant 0.15
PPE35 2169594 p.Gly340Val missense_variant 0.11
PPE35 2169940 p.Gly225Cys missense_variant 0.2
PPE35 2170280 c.333C>G synonymous_variant 0.17
PPE35 2170298 c.315A>G synonymous_variant 0.17
Rv1979c 2223219 c.-55T>C upstream_gene_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288761 p.Ala161Ser missense_variant 0.15
pncA 2288794 p.Gly150Ser missense_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518256 p.Asp48Tyr missense_variant 0.2
kasA 2518466 p.Gly118Arg missense_variant 0.17
kasA 2518568 p.Ala152Ser missense_variant 0.25
kasA 2518809 p.Lys232Arg missense_variant 0.14
kasA 2519041 c.927C>T synonymous_variant 0.15
kasA 2519329 c.1215C>T synonymous_variant 0.29
folC 2746188 p.Ser471Pro missense_variant 0.29
folC 2746335 p.Gly422Ser missense_variant 0.17
folC 2746339 c.1260G>C synonymous_variant 0.17
folC 2746343 p.Leu419Pro missense_variant 0.17
folC 2746494 p.Glu369Lys missense_variant 0.14
pepQ 2859314 c.1105C>T synonymous_variant 0.11
pepQ 2859603 c.816G>T synonymous_variant 0.25
ribD 2986857 p.Leu7Phe missense_variant 0.13
Rv2752c 3064519 p.Val558Ala missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087476 p.Tyr219* stop_gained 0.13
ald 3087917 c.1099delG frameshift_variant 0.15
ald 3087924 p.Val369Met missense_variant 0.15
Rv3083 3448864 p.Val121Leu missense_variant 0.29
fprA 3473956 c.-51C>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474307 p.Ile101Val missense_variant 0.17
fprA 3475197 c.1191C>T synonymous_variant 0.22
fbiB 3641665 p.Asp44Ala missense_variant 0.18
fbiB 3641668 p.Val45Ala missense_variant 0.18
alr 3840208 p.Ala405Ser missense_variant 0.13
alr 3841211 c.210C>T synonymous_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.12
ddn 3986779 c.-65A>T upstream_gene_variant 0.14
ddn 3987048 p.Asp69Tyr missense_variant 0.12
clpC1 4038982 p.Asp575His missense_variant 0.14
panD 4043893 p.Glu130Val missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4242977 c.-256C>T upstream_gene_variant 0.11
embA 4243671 p.Gly147Cys missense_variant 0.33
embA 4244093 c.861C>A synonymous_variant 0.18
embA 4244452 p.Pro407Leu missense_variant 0.22
embA 4244456 c.1224C>A synonymous_variant 0.22
embA 4244461 p.Val410Ala missense_variant 0.22
embA 4244994 p.Thr588Ala missense_variant 0.18
embB 4246633 p.Leu40Phe missense_variant 0.22
embB 4246791 p.Pro93Arg missense_variant 0.15
embB 4247892 p.Arg460His missense_variant 0.33
embB 4248774 p.Leu754Arg missense_variant 0.15
aftB 4267232 c.1605C>T synonymous_variant 0.12
ubiA 4269168 p.Trp222Cys missense_variant 0.12
aftB 4269492 c.-656G>A upstream_gene_variant 0.14
ubiA 4269647 p.Ser63Gly missense_variant 0.12
ethA 4327007 p.Asp156Gly missense_variant 0.12
ethA 4327223 p.Tyr84Cys missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407657 c.546C>T synonymous_variant 0.12