TB-Profiler result

Run: ERR4818945
Summary

Run ID: ERR4818945

Sample name:

Date: 01-04-2023 15:50:21

Number of reads: 755062

Percentage reads mapped: 96.55

Strain: lineage4.1.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.3 Euro-American T;X;H None 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 1472733 n.888G>A non_coding_transcript_exon_variant 0.27 streptomycin
pncA 2289225 p.Ile6Thr missense_variant 0.15 pyrazinamide
ethA 4327132 c.341delA frameshift_variant 0.12 ethionamide, ethionamide
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 5704 c.465C>A synonymous_variant 0.13
gyrB 6086 p.Thr283Ala missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8475 p.Arg392Cys missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575391 p.Gln15Arg missense_variant 0.15
mshA 575770 c.423G>T synonymous_variant 0.13
mshA 575804 p.Ser153Pro missense_variant 0.12
ccsA 619703 c.-188C>T upstream_gene_variant 0.14
ccsA 619767 c.-124C>T upstream_gene_variant 0.17
ccsA 620514 c.625_626dupGA frameshift_variant 0.12
rpoB 761906 c.2100C>G synonymous_variant 0.11
rpoB 761909 c.2103T>C synonymous_variant 0.11
rpoB 761912 c.2106T>C synonymous_variant 0.12
rpoB 761915 p.Asp703Glu missense_variant 0.12
rpoB 761916 p.Asp704Asn missense_variant 0.12
rpoB 761921 c.2115C>T synonymous_variant 0.14
rpoB 761951 c.2145G>C synonymous_variant 0.22
rpoB 761954 c.2148C>G synonymous_variant 0.2
rpoB 761955 p.Ile717Val missense_variant 0.2
rpoB 762555 p.Pro917Ala missense_variant 0.14
rpoC 763061 c.-309C>A upstream_gene_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766005 p.Asp879Gly missense_variant 0.17
rpoC 766129 c.2760C>G synonymous_variant 0.11
rpoC 766135 c.2766G>A synonymous_variant 0.11
rpoC 766148 p.Thr927Ala missense_variant 0.1
rpoC 766211 c.2843delA frameshift_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775663 p.Pro940Thr missense_variant 0.14
mmpL5 778053 p.Asp143Gly missense_variant 0.12
mmpL5 778612 c.-132C>T upstream_gene_variant 0.25
mmpR5 779318 c.331delA frameshift_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
fbiC 1303097 p.Ala56Val missense_variant 0.15
fbiC 1304610 c.1680C>T synonymous_variant 1.0
Rv1258c 1406136 p.Glu402Gly missense_variant 0.12
Rv1258c 1407345 c.-5T>C upstream_gene_variant 0.2
embR 1416453 p.Arg299Cys missense_variant 0.12
embR 1416928 c.420C>T synonymous_variant 0.14
embR 1417043 p.Arg102Gln missense_variant 0.11
atpE 1461074 c.30C>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.15
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.14
rrs 1472543 n.699_700delCA non_coding_transcript_exon_variant 0.21
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.42
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.4
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.42
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.42
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.4
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.3
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.3
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.33
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.11
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.31
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.29
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.29
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.22
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.22
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.18
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.15
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.23
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.23
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.14
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.12
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.25
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.12
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.17
rrs 1473314 n.1469A>G non_coding_transcript_exon_variant 0.18
rrl 1473640 n.-17delT upstream_gene_variant 0.22
rrl 1473736 n.82_83dupGG non_coding_transcript_exon_variant 0.13
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.14
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.14
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>A non_coding_transcript_exon_variant 0.13
inhA 1674257 p.Ser19Leu missense_variant 0.11
inhA 1674320 p.Gly40Glu missense_variant 0.14
rpsA 1833808 c.267G>T synonymous_variant 0.15
rpsA 1833811 c.270G>T synonymous_variant 0.13
rpsA 1833832 c.291G>A synonymous_variant 0.13
rpsA 1833838 c.297G>T synonymous_variant 0.12
rpsA 1833841 c.300C>G synonymous_variant 0.11
rpsA 1833847 c.306C>G synonymous_variant 0.12
rpsA 1833856 c.315A>G synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918046 p.Gly36Val missense_variant 0.13
tlyA 1918560 c.621G>T synonymous_variant 0.14
katG 2153968 p.Asp715Gly missense_variant 0.2
PPE35 2167650 c.2963A>G splice_region_variant&stop_retained_variant 0.13
PPE35 2167877 p.Ser912Arg missense_variant 0.12
PPE35 2168260 c.2352delT frameshift_variant 0.12
PPE35 2169788 p.Leu275Phe missense_variant 0.12
PPE35 2170083 p.Gly177Val missense_variant 0.25
PPE35 2170232 c.381T>C synonymous_variant 0.11
Rv1979c 2222745 c.420G>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289285 c.-44G>T upstream_gene_variant 0.11
pncA 2289901 c.-660G>A upstream_gene_variant 0.18
kasA 2517925 c.-189delG upstream_gene_variant 0.11
kasA 2518225 c.111G>A synonymous_variant 0.12
kasA 2518240 c.126C>A synonymous_variant 0.15
eis 2714346 c.987C>T synonymous_variant 0.12
folC 2746579 c.1020G>A synonymous_variant 0.12
folC 2747247 p.Ala118Thr missense_variant 0.13
folC 2747549 p.Val17Ala missense_variant 0.17
pepQ 2860307 p.Gly38Trp missense_variant 0.14
pepQ 2860364 c.54dupG frameshift_variant 0.13
pepQ 2860404 p.Gln5His missense_variant 0.12
pepQ 2860561 c.-143C>A upstream_gene_variant 0.13
ribD 2987034 p.Gly66Ser missense_variant 0.14
Rv2752c 3067056 c.-865T>C upstream_gene_variant 0.11
thyA 3074296 p.Leu59Pro missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448783 p.Val94Phe missense_variant 0.13
Rv3083 3449845 p.Gln448* stop_gained 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475332 c.1326C>T synonymous_variant 0.14
fbiB 3641109 c.-426C>G upstream_gene_variant 0.13
fbiB 3642483 p.Trp317Arg missense_variant 0.15
rpoA 3878679 c.-172G>A upstream_gene_variant 0.22
clpC1 4039561 p.Ala382Thr missense_variant 0.15
clpC1 4040218 p.Gly163Ser missense_variant 0.13
embC 4240643 c.781C>A synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243337 c.105G>T synonymous_variant 0.12
embA 4244279 c.1047G>T synonymous_variant 0.12
embB 4248413 p.Phe634Leu missense_variant 0.17
embB 4249605 p.Gly1031Asp missense_variant 0.13
embB 4249655 p.Val1048Ile missense_variant 0.29
aftB 4268683 p.Gly52Ser missense_variant 1.0
aftB 4268775 p.Ser21Ile missense_variant 0.15
aftB 4268871 c.-35G>T upstream_gene_variant 0.22
ethA 4327050 c.421_423dupTAC conservative_inframe_insertion 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407855 c.348G>C synonymous_variant 0.13
gid 4408032 p.Glu57Asp missense_variant 0.11