TB-Profiler result

Run: SRR6982440
Summary

Run ID: SRR6982440

Sample name:

Date: 04-04-2023 18:37:27

Number of reads: 266398

Percentage reads mapped: 99.53

Strain: lineage4.3.4.2.1

Drug-resistance: MDR-TB

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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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490840 p.Leu20Phe missense_variant 0.18
fgd1 491134 c.353delA frameshift_variant 0.17
mshA 575913 p.Ala189Val missense_variant 0.18
mshA 576370 c.1023G>A synonymous_variant 0.33
rpoB 760598 c.792C>A synonymous_variant 0.17
rpoB 761147 c.1341C>T synonymous_variant 0.1
rpoB 762362 p.Glu852Asp missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766207 p.Asp946Glu missense_variant 0.11
rpoC 766362 p.Val998Ala missense_variant 0.17
rpoC 766467 p.Glu1033Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779650 c.-773_-746delTGCGAACAACAAGATCGCCTTCGACAGG upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476651 n.2994T>C non_coding_transcript_exon_variant 0.15
inhA 1673435 c.-767T>C upstream_gene_variant 0.2
fabG1 1673924 p.Gly162Val missense_variant 0.11
rpsA 1834972 c.1431C>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155079 p.Lys345* stop_gained 0.18
PPE35 2168322 p.Ile764Thr missense_variant 0.25
PPE35 2168531 c.2082G>T synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.16
PPE35 2170795 c.-183G>T upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289240 c.2T>A start_lost 0.11
kasA 2517921 c.-194A>G upstream_gene_variant 0.18
kasA 2519110 p.Asp332Glu missense_variant 0.22
folC 2746196 p.Ile468Asn missense_variant 0.12
folC 2747787 c.-189C>T upstream_gene_variant 0.14
pepQ 2859915 c.504C>A synonymous_variant 0.12
Rv2752c 3067032 c.-841C>T upstream_gene_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612605 p.Val171Ala missense_variant 0.2
Rv3236c 3612704 p.Glu138Gly missense_variant 0.29
fbiA 3641224 p.Gly228Arg missense_variant 0.12
fbiB 3642877 p.Lys448Arg missense_variant 0.18
alr 3840378 p.Val348Ala missense_variant 0.11
alr 3840719 c.702A>G synonymous_variant 1.0
ddn 3987075 p.Ser78Pro missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039431 p.Asp425Val missense_variant 0.15
embC 4240962 p.Leu367Arg missense_variant 0.15
embC 4241633 p.Gly591Arg missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243246 c.15delT frameshift_variant 0.4
embA 4243635 p.Gly135Ser missense_variant 0.1
embA 4246174 p.Ile981Asn missense_variant 0.5
embB 4247671 c.1158G>A synonymous_variant 0.11
ethA 4327875 c.-402C>G upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407714 c.489A>G synonymous_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0