TB-Profiler result

Run: ERR403413
Summary

Run ID: ERR403413

Sample name:

Date: 01-04-2023 04:28:22

Number of reads: 305964

Percentage reads mapped: 99.42

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.98
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
gyrB 5662 c.423C>T synonymous_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7643 c.342C>T synonymous_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.23
mshA 575585 p.Ala80Thr missense_variant 0.33
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576281 p.Leu312Met missense_variant 0.25
mshA 576293 p.Ala316Pro missense_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762006 p.Arg734Ser missense_variant 0.22
rpoC 764330 p.Pro321Ser missense_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778694 p.Tyr71Ser missense_variant 0.25
mmpS5 779591 c.-686C>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304159 p.Val410Gly missense_variant 0.5
Rv1258c 1406254 p.Gly363Ser missense_variant 0.33
Rv1258c 1406274 p.Ala356Val missense_variant 0.4
Rv1258c 1406322 p.Ala340Val missense_variant 0.4
Rv1258c 1406400 p.Ile314Thr missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.14
rpsA 1834273 p.His244Gln missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102827 c.216C>T synonymous_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 0.38
katG 2155856 p.Thr86Pro missense_variant 0.43
katG 2156453 c.-342C>T upstream_gene_variant 0.25
PPE35 2168499 p.Ser705Leu missense_variant 0.18
PPE35 2169320 p.Leu431Phe missense_variant 0.5
PPE35 2169862 p.Asn251His missense_variant 0.6
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518967 p.Val285Ile missense_variant 0.33
kasA 2519326 c.1212C>T synonymous_variant 0.33
ahpC 2725959 c.-234C>G upstream_gene_variant 0.22
folC 2747770 c.-172T>C upstream_gene_variant 0.22
pepQ 2859536 p.Gly295* stop_gained 0.25
Rv2752c 3064585 p.Thr536Met missense_variant 0.13
Rv2752c 3064676 p.Pro506Ser missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087604 p.Ala262Glu missense_variant 0.18
Rv3083 3448995 c.492G>A synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474525 p.Leu173Phe missense_variant 0.5
fbiA 3641245 p.Glu235Gln missense_variant 0.4
fbiB 3641784 p.Arg84Cys missense_variant 0.4
alr 3841473 c.-53G>A upstream_gene_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.5
clpC1 4038562 p.Asp715Asn missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243111 c.-122C>T upstream_gene_variant 0.25
embA 4244897 c.1665T>A synonymous_variant 0.25
embB 4246840 c.327C>A synonymous_variant 0.25
aftB 4267089 p.Thr583Asn missense_variant 0.93
whiB6 4338595 c.-75delG upstream_gene_variant 1.0