TB-Profiler result

Run: ERR2229438
Summary

Run ID: ERR2229438

Sample name:

Date: 31-03-2023 17:12:13

Number of reads: 925782

Percentage reads mapped: 99.03

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
mshA 575311 c.-37A>G upstream_gene_variant 0.29
mshA 576104 p.Arg253Ser missense_variant 0.25
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576589 c.1242A>G synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776244 p.Ile746Thr missense_variant 0.2
mmpL5 776996 c.1485C>G synonymous_variant 0.11
mmpL5 777149 p.Asn444Lys missense_variant 0.14
mmpL5 777157 c.1324C>A synonymous_variant 0.12
mmpL5 777164 c.1317C>T synonymous_variant 0.14
mmpL5 777176 p.Glu435Asp missense_variant 0.15
mmpS5 778626 c.279_280insGTGAGCG frameshift_variant 0.18
mmpS5 778630 p.Leu92Phe missense_variant 0.18
mmpS5 778632 c.267_273delGCTCACC frameshift_variant 0.22
mmpS5 778646 c.252_259delAGCCCTGC frameshift_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781810 p.Gly84Asp missense_variant 0.14
rplC 801292 p.Lys162Glu missense_variant 0.13
fbiC 1303573 p.Leu215Met missense_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407097 p.Ser82Pro missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474654 n.997C>A non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.17
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673357 c.-83G>A upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.13
PPE35 2167868 c.2745A>C synonymous_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.12
PPE35 2167982 c.2630delG frameshift_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169602 c.1011C>A synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.19
PPE35 2170147 p.Ser156Ala missense_variant 0.24
PPE35 2170157 p.Ala152Ser missense_variant 0.2
PPE35 2170385 c.228G>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518348 c.234A>T synonymous_variant 0.17
kasA 2518864 c.750G>C synonymous_variant 0.2
eis 2714307 c.1025dupC frameshift_variant 0.22
eis 2714347 p.Phe329Tyr missense_variant 0.12
pepQ 2859962 p.Ala153Thr missense_variant 0.12
Rv2752c 3064862 p.Val444Met missense_variant 0.12
Rv2752c 3066309 c.-119dupG upstream_gene_variant 0.15
Rv2752c 3067145 c.-954C>A upstream_gene_variant 0.14
fbiD 3339218 p.Thr34Ile missense_variant 0.17
fprA 3473944 c.-63A>G upstream_gene_variant 0.11
Rv3236c 3612727 c.390G>T synonymous_variant 0.14
alr 3840211 p.Glu404Lys missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.18
rpoA 3878567 c.-60C>G upstream_gene_variant 1.0
clpC1 4039691 c.1014G>C synonymous_variant 0.18
clpC1 4040010 p.Ala232Arg missense_variant 0.12
clpC1 4040021 c.684A>C synonymous_variant 0.13
clpC1 4040024 c.681A>G synonymous_variant 0.18
clpC1 4040218 p.Gly163Cys missense_variant 0.25
embC 4241791 c.1929G>T synonymous_variant 0.12
embC 4241807 p.Pro649Thr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243092 p.Leu1077Arg missense_variant 0.11
embA 4243096 c.-137A>C upstream_gene_variant 0.11
embA 4243099 c.-134G>C upstream_gene_variant 0.12
embA 4243102 c.-131G>T upstream_gene_variant 0.12
embC 4243103 p.Thr1081Pro missense_variant 0.12
embC 4243106 p.Arg1082Ser missense_variant 0.12
embA 4243302 p.Gly24Cys missense_variant 0.15
embA 4244679 p.Ala483Thr missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Arg missense_variant 0.18
embB 4246563 p.Leu17Trp missense_variant 0.22
embB 4247028 p.Leu172Arg missense_variant 0.2
embB 4248822 p.Asp770Val missense_variant 0.2
aftB 4268443 p.Arg132Ser missense_variant 0.2
aftB 4268792 c.45G>A synonymous_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_variant 0.16
ethR 4326982 c.-567C>G upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0