TB-Profiler result

Run: ERR2229693
Summary

Run ID: ERR2229693

Sample name:

Date: 31-03-2023 17:26:29

Number of reads: 543621

Percentage reads mapped: 99.14

Strain: lineage4

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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
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
katG 2154921 p.Trp397* stop_gained 0.17 isoniazid
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 5724 p.Ala162Val missense_variant 0.18
gyrB 6219 p.Val327Ala missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8462 c.1161A>G synonymous_variant 0.2
gyrA 9054 p.Pro585Thr missense_variant 0.12
ccsA 620667 p.Trp259Cys missense_variant 0.18
ccsA 620795 p.Ala302Asp missense_variant 0.17
rpoB 759939 p.Pro45Ser missense_variant 0.17
rpoC 764460 p.Glu364Val missense_variant 0.17
rpoC 765635 p.Val756Phe missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776361 p.Gln707Arg missense_variant 0.14
mmpL5 777091 p.Val464Leu missense_variant 0.2
mmpR5 779237 p.Leu83Arg missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781438 c.-122A>T upstream_gene_variant 0.17
rpsL 781758 p.Ile67Val missense_variant 0.15
fbiC 1303509 c.579G>T synonymous_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406514 p.Leu276Pro missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473542 n.-116C>A upstream_gene_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.39
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.22
PPE35 2167967 c.2646A>C synonymous_variant 0.25
PPE35 2168475 p.Pro713Gly missense_variant 0.12
PPE35 2168482 p.Val711Leu missense_variant 0.15
PPE35 2168596 p.Phe673Leu missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169044 c.1569G>C synonymous_variant 0.25
PPE35 2169269 c.1344A>G synonymous_variant 0.17
PPE35 2169272 c.1341C>G synonymous_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.18
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.64
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288992 p.Ser84Gly missense_variant 0.17
kasA 2518606 c.492G>C synonymous_variant 0.4
kasA 2518609 p.Met165Ile missense_variant 0.4
kasA 2519220 p.Pro369Gln missense_variant 0.4
kasA 2519240 p.Pro376Thr missense_variant 0.25
eis 2715175 p.Gly53Asp missense_variant 0.18
ahpC 2725938 c.-255_-254insA upstream_gene_variant 0.14
ahpC 2726470 c.281dupT frameshift_variant 0.15
ribD 2986702 c.-137G>T upstream_gene_variant 0.17
ribD 2986703 c.-136A>T upstream_gene_variant 0.18
Rv2752c 3064896 c.1296T>C synonymous_variant 0.29
Rv2752c 3065438 p.Ala252Thr missense_variant 0.15
thyX 3068023 c.-78C>T upstream_gene_variant 0.25
thyA 3073881 c.591C>T synonymous_variant 0.15
ald 3086673 c.-147G>T upstream_gene_variant 0.18
fprA 3474626 p.Phe207Ser missense_variant 0.29
fprA 3475061 p.Pro352His missense_variant 0.29
Rv3236c 3612623 p.Tyr165Phe missense_variant 0.29
fbiB 3640872 c.-663C>T upstream_gene_variant 0.4
fbiB 3642807 p.Ala425Ser missense_variant 0.22
alr 3840948 p.Val158Ala missense_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.19
ddn 3987017 p.Gln58His missense_variant 0.17
ddn 3987205 p.Glu121Gly missense_variant 0.13
clpC1 4040137 p.Val190Ile missense_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.13
embC 4241728 p.Phe622Leu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.29
embB 4246544 p.Thr11Pro missense_variant 0.6
embB 4247046 p.Asp178Ala missense_variant 0.5
aftB 4268045 p.Tyr264* stop_gained 0.2
ethA 4326340 c.1134C>A synonymous_variant 0.14
ethA 4326394 c.1080A>G synonymous_variant 0.25
ethA 4328240 c.-767T>C upstream_gene_variant 0.14
ethA 4328458 c.-985C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408204 c.-2T>C upstream_gene_variant 0.18