TB-Profiler result

Run: ERR2229428
Summary

Run ID: ERR2229428

Sample name:

Date: 31-03-2023 17:11:03

Number of reads: 767153

Percentage reads mapped: 99.19

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 575383 c.36G>A synonymous_variant 0.18
mshA 576488 p.Val381His missense_variant 0.29
mshA 576546 p.Asp400Gly missense_variant 0.18
rpoB 759714 c.-93C>A upstream_gene_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775715 c.2766G>A synonymous_variant 0.12
mmpL5 775718 c.2763C>G synonymous_variant 0.12
mmpL5 775726 c.2755C>T synonymous_variant 0.18
mmpL5 775727 c.2754C>G synonymous_variant 0.18
mmpL5 776554 p.Gln643Lys missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303606 p.Lys226Glu missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305212 p.Pro761His missense_variant 0.13
embR 1417284 p.Thr22Ser 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
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
rpsA 1833392 c.-150C>A upstream_gene_variant 0.14
rpsA 1833480 c.-62G>T upstream_gene_variant 0.12
rpsA 1834112 p.Leu191Met missense_variant 0.18
tlyA 1917841 c.-99C>A upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101825 c.1218G>T synonymous_variant 0.14
katG 2155127 p.Asp329Asn missense_variant 0.12
PPE35 2167814 c.2799C>T synonymous_variant 0.17
PPE35 2168047 p.Leu856Val missense_variant 0.12
PPE35 2168051 c.2562G>C synonymous_variant 0.12
PPE35 2168068 p.Phe849Leu missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2169278 c.1335T>C synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.15
PPE35 2169828 p.Ala262Val missense_variant 0.12
PPE35 2169902 c.711G>C synonymous_variant 0.17
PPE35 2169910 p.Asn235Tyr missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.39
PPE35 2170053 p.Thr187Ser missense_variant 0.43
Rv1979c 2222415 c.750G>T synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290133 c.-892C>A upstream_gene_variant 0.18
kasA 2518864 c.750G>C synonymous_variant 0.33
kasA 2519140 c.1026G>C synonymous_variant 0.2
kasA 2519143 c.1029G>C synonymous_variant 0.2
eis 2714410 p.Arg308Leu missense_variant 0.17
eis 2714922 p.Leu137Phe missense_variant 0.18
eis 2715060 p.His91Gln missense_variant 0.11
eis 2715065 p.Thr90Ala missense_variant 0.11
ahpC 2726741 c.549G>T synonymous_variant 0.12
ahpC 2726755 p.Gly188Asp missense_variant 0.14
folC 2746999 p.Asp200Glu missense_variant 0.13
folC 2747216 p.Glu128Gly missense_variant 0.13
folC 2747488 c.111C>A synonymous_variant 0.33
thyA 3073892 c.580T>C synonymous_variant 0.12
ald 3086997 p.Thr60Gly missense_variant 0.13
fbiD 3339495 c.379delG frameshift_variant 0.17
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568476 c.204T>C synonymous_variant 0.11
whiB7 3568780 c.-101A>G upstream_gene_variant 0.11
whiB7 3568788 c.-109G>T upstream_gene_variant 0.12
whiB7 3568789 c.-110A>C upstream_gene_variant 0.12
Rv3236c 3612226 c.891G>T synonymous_variant 0.15
fbiB 3642292 p.Arg253Leu missense_variant 0.22
fbiB 3642506 c.972C>T synonymous_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.26
rpoA 3878178 p.Ile110Met missense_variant 0.11
rpoA 3878551 c.-44C>T upstream_gene_variant 0.4
clpC1 4039508 c.1197G>C synonymous_variant 0.16
clpC1 4039682 c.1023C>T synonymous_variant 0.13
panD 4043955 p.Asp109Glu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246166 p.Leu978Phe missense_variant 0.25
embA 4246389 p.Asp1053Tyr missense_variant 0.12
embB 4247512 c.999T>C synonymous_variant 0.18
embB 4247516 p.Asn335Asp missense_variant 0.2
embB 4248909 p.Ala799Asp missense_variant 0.12
embB 4249741 c.3228C>A synonymous_variant 0.17
embB 4249760 p.Ala1083Thr missense_variant 0.14
aftB 4268499 c.337delC frameshift_variant 0.33
ubiA 4269469 p.Pro122Gln missense_variant 0.17
ubiA 4269518 p.Ala106Thr missense_variant 0.15
ubiA 4269766 p.Pro23Leu missense_variant 0.14
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4326964 c.-585G>A upstream_gene_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408079 p.Gly42Cys missense_variant 0.12
fgd1 433970 c.-56812_*39805del transcript_ablation 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0