TB-Profiler result

Run: ERR2229553

Summary

Run ID: ERR2229553

Sample name:

Date: 31-03-2023 17:18:43

Number of reads: 802022

Percentage reads mapped: 93.79

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491528 p.Trp249Leu missense_variant 0.13
mshA 576260 p.Gly305Ser missense_variant 0.4
mshA 576337 c.990G>T synonymous_variant 0.15
ccsA 620202 c.312G>A synonymous_variant 0.12
rpoB 761526 p.Asp574His missense_variant 0.12
rpoC 764367 p.Gly333Ala missense_variant 0.25
rpoC 766194 p.Gln942Arg missense_variant 0.17
rpoC 766330 p.Lys987Asn missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775727 c.2754C>G synonymous_variant 0.12
mmpL5 776274 p.Ala736Asp missense_variant 0.14
mmpL5 777136 p.Met449Leu missense_variant 0.12
mmpL5 777884 c.597C>G synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800688 c.-121C>A upstream_gene_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304982 c.2052G>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.12
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.12
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.12
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.12
rrl 1476206 n.2549A>G non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
rpsA 1834094 p.Leu185Met missense_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103051 c.-9C>A upstream_gene_variant 0.14
katG 2155629 p.Trp161Cys missense_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2169910 p.Asn235Tyr missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2221850 p.Leu439Ile missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518771 c.657C>T synonymous_variant 0.33
kasA 2518864 c.750G>C synonymous_variant 0.17
eis 2715138 p.Met65Ile missense_variant 0.12
folC 2747077 p.Glu174Asp missense_variant 0.15
Rv2752c 3065027 c.1165C>A synonymous_variant 0.2
Rv2752c 3065486 p.Ala236Ser missense_variant 0.12
thyX 3067418 c.528C>A synonymous_variant 0.13
thyA 3074553 c.-82C>A upstream_gene_variant 0.17
fprA 3474323 p.Ala106Glu missense_variant 0.17
Rv3236c 3612271 c.846T>C synonymous_variant 0.17
Rv3236c 3612962 p.Ala52Asp missense_variant 0.14
clpC1 4038563 c.2142C>T synonymous_variant 0.12
clpC1 4038773 p.Asp644Glu missense_variant 0.15
clpC1 4038776 p.Glu643Asp missense_variant 0.15
clpC1 4039829 p.Leu292Phe missense_variant 0.12
clpC1 4040404 p.Asn101Tyr missense_variant 0.22
panD 4044156 p.Glu42Asp missense_variant 0.15
embC 4241076 p.Gly405Asp missense_variant 0.12
embC 4241533 c.1671T>A synonymous_variant 0.13
embC 4241578 c.1716G>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243519 p.Gly96Asp missense_variant 0.12
embA 4245274 p.Arg681Leu missense_variant 0.12
embA 4246077 p.Ser949Gly missense_variant 0.2
embB 4246766 p.Cys85Ser missense_variant 0.17
embB 4246790 p.Pro93Ser missense_variant 0.15
embB 4247392 c.879C>T synonymous_variant 0.18
aftB 4267691 c.1145delT frameshift_variant 0.2
aftB 4268619 p.Val73Gly missense_variant 0.25
ubiA 4269485 p.Ala117Ser missense_variant 0.2
ethR 4326961 c.-588G>C upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.15
ethR 4326970 c.-579G>T upstream_gene_variant 0.14
ethA 4327517 c.-44A>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0