TB-Profiler result

Run: ERR2229391
Summary

Run ID: ERR2229391

Sample name:

Date: 31-03-2023 17:08:59

Number of reads: 571576

Percentage reads mapped: 98.82

Strain: lineage4.8

Drug-resistance: Other

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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
tlyA 1918342 c.404_405delAC frameshift_variant 0.29 capreomycin
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
gyrB 5959 c.720C>G synonymous_variant 0.25
gyrB 6701 p.Val488Leu missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8092 p.Arg264Leu missense_variant 0.12
fgd1 490853 p.Ala24Asp missense_variant 0.12
rpoB 759977 p.Trp57* stop_gained 0.2
rpoB 761157 p.Ala451Ser missense_variant 0.25
rpoB 763106 p.Ile1100Met missense_variant 0.2
rpoC 763775 p.Ile136Phe missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775881 p.Asn867Ser missense_variant 0.33
mmpL5 776222 c.2258delG frameshift_variant 0.5
mmpL5 777061 p.Ala474Pro missense_variant 0.18
mmpL5 778926 c.-446A>G upstream_gene_variant 0.17
mmpR5 779121 c.138_139dupTG frameshift_variant 0.33
mmpS5 779661 c.-756C>A upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.18
rrl 1474644 n.987G>A non_coding_transcript_exon_variant 0.2
rrl 1474925 n.1268G>T non_coding_transcript_exon_variant 0.29
rrl 1475506 n.1849A>G non_coding_transcript_exon_variant 0.4
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.42
rpsA 1834047 p.Ile169Thr missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918150 p.Val71Phe missense_variant 0.17
ndh 2102751 p.Cys98Ser missense_variant 0.22
katG 2154193 p.Arg640His missense_variant 0.33
katG 2155083 c.1029G>A synonymous_variant 0.14
katG 2155355 c.757C>A synonymous_variant 0.18
katG 2155813 p.Pro100Leu missense_variant 0.4
katG 2156387 c.-276T>A upstream_gene_variant 0.2
PPE35 2167745 p.Thr956Arg missense_variant 0.18
PPE35 2167814 c.2799C>T synonymous_variant 0.2
PPE35 2168622 p.Ala664Asp missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.16
PPE35 2169281 c.1332T>G synonymous_variant 0.21
PPE35 2169287 c.1326T>C synonymous_variant 0.21
PPE35 2169351 p.Ala421His missense_variant 0.17
PPE35 2169587 c.1026G>C synonymous_variant 0.14
PPE35 2169605 c.1008T>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.81
PPE35 2170053 p.Thr187Ser missense_variant 0.85
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289401 c.-160G>T upstream_gene_variant 0.18
kasA 2519128 c.1014G>C synonymous_variant 0.4
kasA 2519131 c.1017G>C synonymous_variant 0.4
kasA 2519140 c.1026G>C synonymous_variant 0.33
kasA 2519143 c.1029G>C synonymous_variant 0.33
eis 2714156 p.Asp393Tyr missense_variant 0.2
ahpC 2725935 c.-258G>T upstream_gene_variant 0.17
ahpC 2726431 p.Ala80Gly missense_variant 0.22
pepQ 2860159 p.Ala87Gly missense_variant 0.18
thyX 3067774 p.Ala58Ser missense_variant 0.29
thyA 3074056 p.Glu139Gly missense_variant 0.33
ald 3086839 p.Thr7Ile missense_variant 0.17
fbiB 3640554 c.-981C>A upstream_gene_variant 0.25
fbiA 3640817 p.Leu92Arg missense_variant 0.25
fbiA 3640888 c.349delC frameshift_variant 0.5
fbiA 3641363 p.Arg274Pro missense_variant 0.15
fbiB 3642594 p.Pro354Ser missense_variant 0.25
alr 3841012 p.Gln137Lys missense_variant 0.33
alr 3841546 c.-126C>A upstream_gene_variant 0.17
rpoA 3878069 p.Val147Phe missense_variant 0.33
clpC1 4039042 p.Ser555Thr missense_variant 0.2
clpC1 4039193 c.1512C>G synonymous_variant 0.29
clpC1 4039205 c.1500C>A synonymous_variant 0.25
clpC1 4039730 c.975C>G synonymous_variant 0.4
clpC1 4040144 c.561G>C synonymous_variant 0.8
panD 4044071 p.Ile71Phe missense_variant 0.22
panD 4044314 c.-33C>A upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242910 p.Phe1016Leu missense_variant 0.29
embC 4243092 p.Leu1077Arg missense_variant 0.12
embA 4243096 c.-137A>C upstream_gene_variant 0.12
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 4243371 p.Gln47Lys missense_variant 0.33
embA 4245235 p.Met668Lys missense_variant 0.33
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.83
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.83
embB 4246563 p.Leu17Trp missense_variant 0.67
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4247426 p.Gly305Thr missense_variant 0.2
embB 4248030 p.Thr506Asn missense_variant 0.18
aftB 4266982 p.Asp619Tyr missense_variant 0.33
aftB 4267761 p.Asp359Gly missense_variant 0.43
ubiA 4269269 p.Ala189Ser missense_variant 0.17
ethR 4326961 c.-588G>C upstream_gene_variant 0.18
ethR 4326964 c.-585G>A upstream_gene_variant 0.18
ethR 4326970 c.-579G>T upstream_gene_variant 0.18
ethA 4328323 c.-850T>C upstream_gene_variant 0.12
whiB6 4338485 p.Asn13Asp missense_variant 0.22
whiB6 4338574 c.-53G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0