TB-Profiler result

Run: ERR2229392
Summary

Run ID: ERR2229392

Sample name:

Date: 31-03-2023 17:09:39

Number of reads: 860376

Percentage reads mapped: 98.94

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
gyrA 7640 p.Gln113His missense_variant 0.12
gyrA 8001 p.Ile234Phe missense_variant 0.14
gyrA 8064 p.Gly255* stop_gained 0.12
mshA 575476 c.129C>T synonymous_variant 0.14
mshA 575929 c.582C>A synonymous_variant 0.22
mshA 576099 p.Asp251Gly missense_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.44
rpoB 761258 c.1452G>A synonymous_variant 0.14
rpoB 761507 c.1701G>A synonymous_variant 0.13
rpoB 762325 p.Lys840Arg missense_variant 0.17
rpoC 762704 c.-666G>A upstream_gene_variant 0.18
rpoC 763656 p.Glu96Gly missense_variant 0.14
rpoC 763920 p.Leu184Gln missense_variant 0.12
rpoC 764136 p.Met256Thr missense_variant 0.12
rpoC 765086 p.Pro573Ala missense_variant 0.12
rpoC 766877 p.Ser1170Pro missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775852 p.Ser877Gly missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302847 c.-84T>A upstream_gene_variant 0.12
fbiC 1303279 p.Gln117Lys missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305500 c.2570A>G stop_lost&splice_region_variant 0.11
Rv1258c 1406874 c.466delG frameshift_variant 0.12
Rv1258c 1407055 c.285delG frameshift_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.41
tlyA 1917885 c.-55G>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102204 p.Val280Asp missense_variant 0.14
ndh 2102786 p.Leu86* stop_gained 0.17
katG 2153997 c.2115G>C synonymous_variant 0.14
katG 2155215 c.897C>T synonymous_variant 0.14
katG 2156047 p.Val22Ala missense_variant 0.12
katG 2156272 c.-161T>C upstream_gene_variant 0.11
PPE35 2167743 p.Gly957Asp missense_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.29
PPE35 2167868 c.2745A>C synonymous_variant 0.32
PPE35 2167996 p.Ser873Cys missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169125 p.Val496Ile missense_variant 0.18
PPE35 2169488 c.1125G>C synonymous_variant 0.18
PPE35 2169491 c.1122T>C synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.81
PPE35 2170053 p.Thr187Ser missense_variant 0.84
Rv1979c 2222279 p.Gly296* stop_gained 0.23
Rv1979c 2222805 c.360G>T synonymous_variant 0.12
Rv1979c 2223075 c.90C>A synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518442 p.Val110Ile missense_variant 0.18
kasA 2518474 c.360G>A synonymous_variant 0.15
kasA 2518537 c.423C>A synonymous_variant 0.13
kasA 2518817 p.Asp235Tyr missense_variant 0.18
kasA 2518864 c.750G>C synonymous_variant 0.18
kasA 2519128 c.1014G>C synonymous_variant 0.13
kasA 2519131 c.1017G>C synonymous_variant 0.12
kasA 2519143 c.1029G>C synonymous_variant 0.14
eis 2715067 p.Pro89Gln missense_variant 0.2
pepQ 2860026 c.393G>T synonymous_variant 0.18
Rv2752c 3065967 p.Glu75Asp missense_variant 0.12
fprA 3474343 p.Asn113Asp missense_variant 0.2
whiB7 3568654 p.Gln9Arg missense_variant 0.14
Rv3236c 3612591 p.Gly176Ser missense_variant 0.15
fbiA 3640565 p.Gly8Ala missense_variant 0.12
fbiB 3642336 p.Thr268Pro missense_variant 0.17
alr 3841183 p.Thr80Ala missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.2
ddn 3986968 p.Gln42Leu missense_variant 0.14
clpC1 4038740 c.1965G>C synonymous_variant 0.12
clpC1 4039277 c.1428C>T synonymous_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243705 p.Gly158Ala missense_variant 0.12
embA 4244861 c.1629G>C synonymous_variant 1.0
embA 4245699 p.Gly823Trp missense_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.59
embB 4246555 c.42G>C synonymous_variant 0.64
embB 4246556 p.Ala15Pro missense_variant 0.64
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4247028 p.Leu172Arg missense_variant 0.5
embB 4247537 p.His342Asp missense_variant 0.12
embB 4248871 c.2358C>T synonymous_variant 0.18
embB 4249711 p.Lys1066Asn missense_variant 0.29
aftB 4267031 c.1806C>A synonymous_variant 0.14
ethA 4326538 c.936G>A synonymous_variant 0.29
ethR 4326679 c.-870C>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407610 p.Pro198Gln missense_variant 0.21
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0