TB-Profiler result

Run: ERR2229579
Summary

Run ID: ERR2229579

Sample name:

Date: 31-03-2023 17:19:57

Number of reads: 393855

Percentage reads mapped: 98.76

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7690 p.Thr130Asn missense_variant 0.4
gyrA 8554 p.Arg418Pro missense_variant 0.2
gyrA 8827 c.1529delT frameshift_variant 0.22
gyrA 9006 p.Phe569Ile missense_variant 0.33
gyrA 9217 p.Asp639Val missense_variant 0.25
fgd1 490688 c.-95G>T upstream_gene_variant 0.17
fgd1 490718 c.-65G>T upstream_gene_variant 0.22
fgd1 491159 p.Lys126Thr missense_variant 0.17
fgd1 491334 p.Tyr184* stop_gained 0.5
fgd1 491666 p.Glu295Gly missense_variant 0.22
mshA 575418 p.Ala24Gly missense_variant 0.2
mshA 575422 c.77_78delGC frameshift_variant 0.2
mshA 576111 p.Ala255Gly missense_variant 0.5
ccsA 620210 p.Trp107Leu missense_variant 0.29
rpoB 761594 c.1788C>T synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775835 c.2646C>G synonymous_variant 0.4
mmpL5 776532 p.Ala650Val missense_variant 0.2
mmpL5 776689 p.Trp598Arg missense_variant 0.4
mmpL5 778563 c.-83C>A upstream_gene_variant 0.18
mmpS5 779675 c.-770G>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781514 c.-46G>T upstream_gene_variant 0.5
rpsL 781552 c.-8G>A upstream_gene_variant 0.4
rplC 801129 c.321C>T synonymous_variant 0.67
fbiC 1303468 p.Arg180Ser missense_variant 0.2
fbiC 1303588 p.Arg220* stop_gained 0.67
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304505 c.1575G>A synonymous_variant 0.25
Rv1258c 1407219 p.Ala41Asp missense_variant 0.33
embR 1416649 c.699A>G synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471835 n.-11G>T upstream_gene_variant 0.18
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.67
rrs 1473146 n.1301G>A non_coding_transcript_exon_variant 0.25
rrl 1473502 n.-156T>C upstream_gene_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474251 n.594G>T non_coding_transcript_exon_variant 1.0
rrl 1475345 n.1688T>A non_coding_transcript_exon_variant 0.29
fabG1 1673380 c.-60C>G upstream_gene_variant 0.39
rpsA 1833361 c.-181G>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918405 p.Ser156Pro missense_variant 0.5
ndh 2102121 p.Asp308Asn missense_variant 0.33
ndh 2102122 c.921C>A synonymous_variant 0.33
katG 2154210 c.1902C>A synonymous_variant 0.22
katG 2156069 p.Ala15Ser missense_variant 0.33
PPE35 2167890 p.Gly908Val missense_variant 0.5
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169381 p.Trp411Ser missense_variant 0.13
PPE35 2169570 p.Ser348Asn missense_variant 0.15
PPE35 2169602 c.1011C>A synonymous_variant 0.22
PPE35 2169725 c.888T>C synonymous_variant 0.17
PPE35 2169836 c.777A>C synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.45
PPE35 2170517 c.96C>T synonymous_variant 0.25
PPE35 2170527 p.Ser29Val missense_variant 0.25
Rv1979c 2222867 p.Ile100Phe missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518457 p.Gly115Ser missense_variant 0.13
kasA 2519140 c.1026G>C synonymous_variant 0.33
kasA 2519143 c.1029G>C synonymous_variant 0.4
kasA 2519153 p.Ile347Val missense_variant 0.4
eis 2715215 p.Val40Leu missense_variant 0.2
ahpC 2726141 c.-52C>A upstream_gene_variant 0.15
folC 2747377 c.222C>T synonymous_variant 0.29
pepQ 2859574 p.Ala282Gly missense_variant 0.67
ribD 2986665 c.-174G>C upstream_gene_variant 0.29
ribD 2987369 c.531G>T synonymous_variant 0.5
Rv2752c 3065989 p.Glu68Val missense_variant 0.5
thyX 3067852 p.Gly32Arg missense_variant 0.5
ald 3087645 p.Glu276* stop_gained 0.22
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
fprA 3475191 p.Cys395* stop_gained 0.18
alr 3841582 c.-162A>G upstream_gene_variant 0.14
alr 3841612 c.-193_-192insC upstream_gene_variant 0.13
ddn 3987184 p.Ala114Val missense_variant 0.12
clpC1 4040236 p.Gly157Cys missense_variant 0.29
clpC1 4040241 p.Thr155Phe missense_variant 0.25
clpC1 4040249 p.Glu152Gly missense_variant 0.38
clpC1 4040370 p.Leu112Pro missense_variant 0.25
panD 4043961 c.321T>C synonymous_variant 0.4
embC 4239715 c.-148G>C upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244427 p.Ser399Thr missense_variant 0.5
embA 4244670 p.Ala480Thr missense_variant 0.29
embB 4246544 p.Thr11Pro missense_variant 0.43
embB 4246548 p.Pro12Gln missense_variant 0.83
embB 4246555 c.42G>C synonymous_variant 0.62
embB 4246556 p.Ala15Pro missense_variant 0.62
embB 4247333 p.Arg274Cys missense_variant 0.2
embB 4247882 p.Ala457Phe missense_variant 0.14
embB 4247993 p.Phe494Leu missense_variant 0.14
embB 4248317 p.Val602Pro missense_variant 0.33
embB 4248320 p.Gly603Thr missense_variant 0.31
embB 4249699 c.3186T>C synonymous_variant 0.67
aftB 4268405 c.432G>T synonymous_variant 0.29
ethA 4326230 p.Asp415Gly missense_variant 0.15
whiB6 4338304 p.Glu73Val missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0