TB-Profiler result

Run: ERR2229166
Summary

Run ID: ERR2229166

Sample name:

Date: 31-03-2023 16:46:12

Number of reads: 325253

Percentage reads mapped: 98.9

Strain: lineage4

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
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 5493 p.Pro85Gln missense_variant 0.33
gyrB 6627 p.Ala463Asp missense_variant 0.15
gyrA 7341 p.Arg14Trp missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8287 p.Asn329Ile missense_variant 0.2
gyrA 9733 p.Thr811Ile missense_variant 0.4
fgd1 491087 p.Phe102Tyr missense_variant 0.22
rpoC 767198 p.Glu1277* stop_gained 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775662 p.Pro940Leu missense_variant 0.4
mmpL5 775727 c.2754C>T synonymous_variant 0.4
mmpL5 776729 c.1752C>T synonymous_variant 0.33
mmpS5 778578 p.Thr110Ser missense_variant 0.29
mmpS5 778854 p.Val18Leu missense_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303855 p.Ala309Thr missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472354 n.509C>A non_coding_transcript_exon_variant 0.15
rrl 1473435 n.-223C>T upstream_gene_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474310 n.653T>C non_coding_transcript_exon_variant 0.13
rrl 1474739 n.1082G>T non_coding_transcript_exon_variant 0.29
rrl 1475610 n.1953G>T non_coding_transcript_exon_variant 0.12
rrl 1475904 n.2247G>A non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.29
fabG1 1673349 c.-91G>C upstream_gene_variant 0.29
fabG1 1673357 c.-83G>A upstream_gene_variant 0.57
fabG1 1673359 c.-81T>C upstream_gene_variant 0.57
fabG1 1673361 c.-79C>G upstream_gene_variant 0.57
fabG1 1673380 c.-60C>G upstream_gene_variant 0.71
rpsA 1833703 p.Asp54Glu missense_variant 0.14
tlyA 1917848 c.-92G>A upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102625 p.Ser140Thr missense_variant 0.29
ndh 2102632 c.411C>A synonymous_variant 0.25
ndh 2102753 p.Gln97Arg missense_variant 0.25
PPE35 2167814 c.2799C>T synonymous_variant 0.4
PPE35 2167965 p.Ala883Gly missense_variant 0.33
PPE35 2167967 c.2646A>C synonymous_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169185 c.1428C>T synonymous_variant 0.33
PPE35 2169191 c.1422G>C synonymous_variant 0.4
PPE35 2169581 c.1032C>G synonymous_variant 0.29
PPE35 2169587 c.1026G>A synonymous_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 1.0
PPE35 2170053 p.Thr187Ser missense_variant 1.0
PPE35 2170188 p.Glu142Leu missense_variant 0.29
PPE35 2170403 c.210C>G synonymous_variant 0.67
PPE35 2170406 c.207A>G synonymous_variant 0.67
PPE35 2170592 c.21G>A synonymous_variant 0.29
Rv1979c 2222991 c.174G>A synonymous_variant 0.22
Rv1979c 2223182 c.-18C>A upstream_gene_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289191 c.51C>A synonymous_variant 0.5
pncA 2289885 c.-644C>A upstream_gene_variant 0.5
pncA 2290058 c.-817G>A upstream_gene_variant 0.29
kasA 2518879 c.765A>G synonymous_variant 0.67
eis 2714990 p.Val115Phe missense_variant 0.67
folC 2746654 c.945C>T synonymous_variant 0.5
pepQ 2859711 c.708C>A synonymous_variant 0.4
Rv2752c 3065112 c.1080C>A synonymous_variant 0.15
Rv2752c 3065422 p.Arg257Gln missense_variant 0.33
Rv2752c 3065451 c.741G>A synonymous_variant 0.33
Rv2752c 3066212 c.-21G>A upstream_gene_variant 1.0
Rv2752c 3067161 c.-970C>A upstream_gene_variant 0.33
thyX 3067736 p.Phe70Leu missense_variant 0.25
ald 3087469 p.Thr217Asn missense_variant 0.2
fprA 3475092 c.1086C>A synonymous_variant 0.29
whiB7 3568704 c.-25G>A upstream_gene_variant 0.2
Rv3236c 3613017 p.Pro34Thr missense_variant 0.5
fbiA 3640979 p.Thr146Asn missense_variant 0.25
alr 3840450 p.Gly324Glu missense_variant 0.33
alr 3840808 p.Asp205Tyr missense_variant 0.67
alr 3841546 c.-126C>A upstream_gene_variant 0.36
rpoA 3878490 c.18C>A synonymous_variant 1.0
ddn 3987195 p.Glu118* stop_gained 0.15
ddn 3987278 c.435G>T synonymous_variant 0.12
clpC1 4039714 p.Tyr331His missense_variant 0.2
clpC1 4039730 c.975C>G synonymous_variant 0.15
clpC1 4039850 c.855T>C synonymous_variant 0.25
clpC1 4040144 c.561G>C synonymous_variant 0.4
embC 4240148 p.Gly96Arg missense_variant 0.18
embC 4240306 c.444C>A synonymous_variant 0.4
embC 4240435 p.Tyr191* stop_gained 0.22
embC 4241728 c.1866C>T synonymous_variant 0.4
embB 4246820 p.Pro103Thr missense_variant 1.0
embB 4247593 c.1080G>T synonymous_variant 0.33
embB 4248033 p.Arg507Met missense_variant 0.2
embB 4248051 p.Gly513Val missense_variant 0.22
embB 4248738 p.Ala742Glu missense_variant 0.67
aftB 4269627 c.-791G>T upstream_gene_variant 0.5
ethA 4327151 p.Asp108Val missense_variant 0.14
ethA 4327774 c.-301G>A upstream_gene_variant 0.22
ethR 4328008 p.Asp154Asn missense_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0