TB-Profiler result

Run: ERR2229144
Summary

Run ID: ERR2229144

Sample name:

Date: 31-03-2023 16:44:42

Number of reads: 719112

Percentage reads mapped: 99.41

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
pncA 2288722 c.518_519delAG frameshift_variant 0.15 pyrazinamide
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 491298 c.517delT frameshift_variant 0.12
mshA 576742 c.1395G>A synonymous_variant 0.17
rpoB 760880 c.1074G>A synonymous_variant 0.29
rpoB 761329 p.Thr508Lys missense_variant 0.14
rpoC 764598 p.Gln410Arg missense_variant 0.2
rpoC 766030 c.2661C>A synonymous_variant 0.2
rpoC 766108 p.Asp913Glu missense_variant 0.18
rpoC 766272 p.Cys968Tyr missense_variant 0.12
rpoC 766766 p.His1133Tyr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776390 c.2091C>T synonymous_variant 0.18
mmpL5 777157 c.1324C>A synonymous_variant 0.22
mmpL5 777164 c.1317C>T synonymous_variant 0.25
mmpR5 779038 p.Met17Leu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304245 p.Asp439Tyr missense_variant 0.25
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.2
Rv1258c 1406946 p.Ala132Gly missense_variant 0.2
Rv1258c 1406948 c.391_392delGC 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 1474576 n.919T>A non_coding_transcript_exon_variant 0.18
fabG1 1673414 c.-26_-25insCGCGG upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102071 c.972C>G synonymous_variant 0.17
ndh 2102417 p.Ala209Val missense_variant 0.12
katG 2154552 c.1560C>T synonymous_variant 0.13
katG 2155601 p.Cys171Arg missense_variant 0.11
katG 2155610 p.Ala168Pro missense_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.29
PPE35 2167967 c.2646A>C synonymous_variant 0.31
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.14
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.21
PPE35 2170053 p.Thr187Ser missense_variant 0.22
Rv1979c 2222878 p.Val96Ala missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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 0.25
kasA 2519143 c.1029G>C synonymous_variant 0.25
eis 2714938 p.Gly132Glu missense_variant 0.25
ribD 2987373 p.Val179Leu missense_variant 0.33
Rv2752c 3065716 p.Tyr159Cys missense_variant 0.12
ald 3086700 c.-120G>T upstream_gene_variant 0.15
fbiB 3640650 c.-885C>T upstream_gene_variant 0.13
fbiB 3641981 c.447C>T synonymous_variant 0.25
fbiB 3642787 p.Trp418Leu missense_variant 0.25
alr 3841289 c.132T>C synonymous_variant 0.11
rpoA 3877648 p.Arg287His missense_variant 0.18
clpC1 4039498 p.Ile403Val missense_variant 0.12
clpC1 4039949 c.756G>T synonymous_variant 0.13
clpC1 4040144 c.561G>C synonymous_variant 0.25
clpC1 4040321 c.384C>T synonymous_variant 0.29
embC 4242078 p.Ser739Tyr missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243614 p.Arg128Ser missense_variant 0.17
embA 4244399 c.1167G>T synonymous_variant 0.33
embA 4245557 p.Glu775Asp missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4248433 p.Trp640Cys missense_variant 0.12
aftB 4268344 p.Arg165Cys missense_variant 0.13
ethR 4327447 c.-102G>T upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0