TB-Profiler result

Run: ERR2229418
Summary

Run ID: ERR2229418

Sample name:

Date: 31-03-2023 17:10:20

Number of reads: 258180

Percentage reads mapped: 98.78

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 7316 c.15G>A synonymous_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8899 p.Leu533Pro missense_variant 0.22
fgd1 490605 c.-178G>T upstream_gene_variant 0.17
fgd1 490634 c.-149A>G upstream_gene_variant 0.12
fgd1 491394 c.612C>T synonymous_variant 0.5
fgd1 491511 p.Leu243Phe missense_variant 0.4
rpoB 760221 p.Gly139Ser missense_variant 0.14
rpoB 762396 p.Arg864Ser missense_variant 0.33
rpoB 762502 p.Pro899Leu missense_variant 0.5
rpoC 763794 p.Glu142Val missense_variant 0.33
rpoC 765484 c.2115G>C synonymous_variant 0.33
rpoC 766087 c.2718C>A synonymous_variant 0.5
rpoC 766554 p.Tyr1062Phe missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777049 c.1431delG frameshift_variant 0.25
mmpL5 777164 c.1317C>T synonymous_variant 0.67
mmpL5 777173 c.1308C>T synonymous_variant 0.29
mmpL5 777176 p.Glu435Asp missense_variant 0.29
mmpL5 778245 p.Gly79Val missense_variant 0.17
mmpS5 778581 p.Gly109Ser missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800875 p.Val23Ile missense_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
atpE 1460993 c.-52C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472034 n.189T>C non_coding_transcript_exon_variant 0.33
rrl 1473797 n.140G>T non_coding_transcript_exon_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1834627 c.1086C>A synonymous_variant 0.67
tlyA 1918316 p.Pro126His missense_variant 0.25
tlyA 1918674 c.735G>T synonymous_variant 0.4
ndh 2101838 p.Ala402Val missense_variant 0.29
ndh 2102004 p.Ile347Phe missense_variant 0.22
katG 2154469 p.Gly548Asp missense_variant 0.25
katG 2155683 p.Lys143Asn missense_variant 0.67
PPE35 2168005 p.His870Asn missense_variant 0.4
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169381 p.Trp411Leu missense_variant 0.33
PPE35 2169725 c.888T>C synonymous_variant 0.22
PPE35 2169732 p.Asn294Ser missense_variant 0.18
PPE35 2169748 p.Ile289Phe missense_variant 0.2
PPE35 2169749 c.864A>C synonymous_variant 0.2
PPE35 2169754 p.Phe287Ile missense_variant 0.2
PPE35 2169902 c.711G>C synonymous_variant 0.15
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.56
PPE35 2170053 p.Thr187Ser missense_variant 0.62
PPE35 2170157 p.Ala152Ser missense_variant 0.29
PPE35 2170299 p.Val105Gly missense_variant 0.33
PPE35 2170392 p.Gly74Ala missense_variant 0.25
PPE35 2170400 c.213G>C synonymous_variant 0.22
pncA 2289903 c.-662C>A upstream_gene_variant 0.5
eis 2714301 c.1031delA frameshift_variant 0.33
eis 2714511 c.821dupC frameshift_variant 0.25
folC 2747662 c.-64G>T upstream_gene_variant 0.67
pepQ 2860483 c.-65A>G upstream_gene_variant 0.22
thyX 3067458 p.Arg163Leu missense_variant 1.0
fprA 3474456 c.450C>A synonymous_variant 0.25
fprA 3475163 p.Leu386His missense_variant 0.33
whiB7 3568612 p.Gly23Asp missense_variant 0.4
Rv3236c 3612140 p.Ala326Val missense_variant 0.25
Rv3236c 3612229 c.888C>G synonymous_variant 1.0
Rv3236c 3612766 c.351C>T synonymous_variant 0.4
fbiA 3640480 c.-63C>A upstream_gene_variant 0.4
fbiA 3640930 p.Glu130* stop_gained 0.22
alr 3840875 c.546C>T synonymous_variant 0.67
alr 3841546 c.-126C>A upstream_gene_variant 0.26
alr 3841574 c.-154T>G upstream_gene_variant 0.11
alr 3841608 c.-188A>C upstream_gene_variant 0.12
clpC1 4038764 c.1941C>T synonymous_variant 0.22
clpC1 4039645 p.His354Asp missense_variant 0.5
embC 4241179 c.1317G>T synonymous_variant 0.2
embC 4241369 p.Lys503* stop_gained 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243092 p.Leu1077Pro missense_variant 0.29
embC 4243120 p.Trp1086Cys missense_variant 0.22
embA 4244780 c.1548C>A synonymous_variant 0.67
embA 4246318 p.Pro1029Gln missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246567 c.54_55insT frameshift_variant 0.4
embB 4247825 p.Ala438Thr missense_variant 0.29
embB 4248097 c.1584C>A synonymous_variant 0.17
embB 4248252 p.Gly580Val missense_variant 0.18
aftB 4268124 p.Ser238Asn missense_variant 0.29
aftB 4268505 p.Arg111Leu missense_variant 0.33
ethR 4326961 c.-588G>C upstream_gene_variant 0.5
ethR 4326964 c.-585G>A upstream_gene_variant 0.5
ethR 4326970 c.-579G>T upstream_gene_variant 0.5
ethA 4327130 p.Arg115His missense_variant 0.22
ethR 4327796 p.Ala83Asp missense_variant 0.2
whiB6 4338277 p.Pro82His missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407839 p.Ser122Thr missense_variant 0.29
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0