TB-Profiler result

Run: ERR751300
Summary

Run ID: ERR751300

Sample name:

Date: 02-04-2023 04:23:46

Number of reads: 4439210

Percentage reads mapped: 99.29

Strain: lineage5.3;lineage4.1.2.1

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 0.16
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 0.85
lineage4.1 Euro-American T;X;H None 0.1
lineage5.3 West-Africa 1 AFRI_2;AFRI_3 RD711 0.85
lineage4.1.2 Euro-American T;H None 0.13
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.15
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 6446 p.Ala403Ser missense_variant 0.89
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.89
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 0.82
fgd1 491591 p.Lys270Met missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 0.83
mshA 575679 p.Asn111Ser missense_variant 0.2
ccsA 620476 p.Phe196Leu missense_variant 0.84
rpoC 763031 c.-339T>C upstream_gene_variant 0.91
rpoC 765150 p.Gly594Glu missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.84
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800793 c.-16G>C upstream_gene_variant 0.8
fbiC 1302899 c.-32A>G upstream_gene_variant 0.81
fbiC 1303449 c.519C>T synonymous_variant 0.14
embR 1416481 c.867G>A synonymous_variant 0.9
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474386 n.729G>A non_coding_transcript_exon_variant 0.13
inhA 1673338 c.-864G>A upstream_gene_variant 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 0.91
ndh 2103112 c.-70G>T upstream_gene_variant 0.83
katG 2154724 p.Arg463Leu missense_variant 0.82
PPE35 2167926 p.Leu896Ser missense_variant 0.88
Rv1979c 2223234 c.-70G>A upstream_gene_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290062 c.-821G>A upstream_gene_variant 0.88
kasA 2518076 c.-39C>T upstream_gene_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 0.86
kasA 2518867 p.Glu251Asp missense_variant 0.81
ald 3086788 c.-32T>C upstream_gene_variant 0.15
ald 3086987 p.Gln56His missense_variant 0.8
ald 3087084 c.266delA frameshift_variant 0.78
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 0.91
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.82
alr 3840932 c.489C>T synonymous_variant 0.92
ddn 3986987 c.144G>T synonymous_variant 0.88
ddn 3987180 p.Asp113Asn missense_variant 0.84
clpC1 4040824 c.-120C>T upstream_gene_variant 0.83
embC 4239843 c.-20A>C upstream_gene_variant 0.85
embC 4240671 p.Thr270Ile missense_variant 0.85
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.17
embA 4244220 c.988C>T synonymous_variant 0.82
embA 4244635 p.Val468Ala missense_variant 0.9
embA 4245147 p.Pro639Ser missense_variant 0.88
embB 4247646 p.Glu378Ala missense_variant 0.88
ubiA 4269387 p.Glu149Asp missense_variant 0.86
aftB 4269606 c.-770T>C upstream_gene_variant 0.88
ethA 4327103 p.Gly124Asp missense_variant 0.83
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.88