TB-Profiler result

Run: ERR2229232
Summary

Run ID: ERR2229232

Sample name:

Date: 31-03-2023 16:50:28

Number of reads: 780197

Percentage reads mapped: 99.08

Strain: lineage4.8

Drug-resistance: HR-TB

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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
katG 2155335 p.Asp259Glu missense_variant 0.18 isoniazid
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 491092 c.312_315delCGTG frameshift_variant 0.13
mshA 575831 p.Gly162Cys missense_variant 0.15
mshA 575875 c.528C>T synonymous_variant 0.15
mshA 575907 p.Ala187Glu missense_variant 0.12
mshA 576711 p.Arg455Gln missense_variant 0.13
ccsA 620371 p.Ala161Thr missense_variant 0.15
rpoB 760358 c.552C>A synonymous_variant 0.13
rpoB 762015 p.Glu737Lys missense_variant 0.12
rpoB 762201 p.Lys799* stop_gained 0.18
rpoC 763606 c.237C>A synonymous_variant 0.13
rpoC 763850 p.Ala161Pro missense_variant 0.12
rpoC 764253 p.Arg295Gln missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775646 p.Gln945His missense_variant 0.18
mmpL5 777405 p.Ala359Asp missense_variant 0.11
mmpL5 777824 p.Leu219Phe missense_variant 0.13
mmpL5 778726 c.-246T>C upstream_gene_variant 0.14
mmpS5 778731 p.Glu59Lys missense_variant 0.14
mmpL5 778931 c.-451A>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303160 p.Gly77Glu missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406720 c.621G>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472913 n.1068G>A non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475914 n.2257C>A non_coding_transcript_exon_variant 0.14
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
rpsA 1834487 p.Gly316Cys missense_variant 0.17
tlyA 1917904 c.-36C>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102593 c.450C>A synonymous_variant 0.13
PPE35 2167814 c.2799C>T synonymous_variant 0.23
PPE35 2167865 c.2748G>C synonymous_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 0.18
PPE35 2168343 p.Gly757Val missense_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169233 p.Leu460Phe missense_variant 0.29
PPE35 2169278 c.1335T>C synonymous_variant 0.11
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169587 c.1026G>A synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2222600 p.His189Asn missense_variant 0.14
Rv1979c 2223131 p.His12Asp missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518809 p.Lys232Arg missense_variant 0.19
eis 2714148 c.1185C>A synonymous_variant 0.14
eis 2714796 c.537C>T synonymous_variant 0.25
eis 2715484 c.-152G>C upstream_gene_variant 0.2
ahpC 2726331 p.Trp47Arg missense_variant 0.15
folC 2746543 c.1056C>T synonymous_variant 0.29
folC 2747484 p.Pro39Ser missense_variant 0.22
ribD 2986868 c.30T>C synonymous_variant 0.17
ribD 2987403 p.Arg189Trp missense_variant 0.17
fbiD 3339736 p.Thr207Pro missense_variant 0.25
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fbiB 3642805 p.Ile424Asn missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.35
alr 3841612 c.-193_-192insC upstream_gene_variant 0.19
clpC1 4038460 p.Leu749Met missense_variant 0.12
clpC1 4038773 p.Asp644Glu missense_variant 0.12
clpC1 4038983 p.Asp574Glu missense_variant 0.12
clpC1 4039146 p.Gly520Glu missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.18
clpC1 4039654 p.Thr351Ser missense_variant 0.18
embC 4241357 p.Ala499Ser missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242954 p.Gly1031Val missense_variant 0.18
embA 4244907 p.Gly559Ser missense_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.25
embB 4246563 p.Leu17Trp missense_variant 0.22
embB 4246567 c.54G>T synonymous_variant 0.2
embB 4247070 p.Val186Ala missense_variant 0.14
embB 4248516 p.Val668Asp missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407909 c.294C>G synonymous_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0