TB-Profiler result

Run: SRR4034363
Summary

Run ID: SRR4034363

Sample name:

Date: 04-04-2023 06:44:45

Number of reads: 1441530

Percentage reads mapped: 99.47

Strain: lineage4.1.2

Drug-resistance: HR-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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;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 2155339 p.Asn258Ser missense_variant 0.17 isoniazid
pncA 2289072 c.169delC frameshift_variant 0.12 pyrazinamide, 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
gyrB 5467 p.Glu76Asp missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9639 p.Gly780Ser missense_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575436 p.Pro30Leu missense_variant 0.15
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764848 c.1479G>A synonymous_variant 0.11
rpoC 765053 p.Ser562Pro missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766700 c.3331C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776381 c.2100C>T synonymous_variant 0.11
mmpL5 776663 c.1818C>A synonymous_variant 0.12
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304454 c.1524C>A synonymous_variant 0.22
embR 1417066 p.Leu94Phe missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472567 n.722G>T non_coding_transcript_exon_variant 0.11
rrl 1474164 n.507C>A non_coding_transcript_exon_variant 0.14
rrl 1476688 n.3031C>A non_coding_transcript_exon_variant 0.15
fabG1 1674164 p.Gly242Val missense_variant 0.13
inhA 1674952 p.Pro251Ala missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101660 c.1383G>T synonymous_variant 0.13
PPE35 2168222 c.2390delC frameshift_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518143 p.Gly10Asp missense_variant 0.13
eis 2714511 c.821delC frameshift_variant 0.2
ahpC 2725954 c.-239C>T upstream_gene_variant 0.11
folC 2747470 c.129C>T synonymous_variant 0.12
folC 2747688 c.-90G>T upstream_gene_variant 0.11
ribD 2986928 c.90G>A synonymous_variant 0.11
thyX 3067278 p.Ala223Val missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474315 c.309C>A synonymous_variant 0.17
fprA 3475190 p.Cys395Tyr missense_variant 0.18
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
fbiB 3641403 c.-132C>T upstream_gene_variant 0.14
fbiA 3641464 p.Leu308Met missense_variant 0.18
fbiB 3642638 c.1104C>A synonymous_variant 0.12
fbiB 3642695 c.1161G>T synonymous_variant 0.12
alr 3840221 p.Arg400Ser missense_variant 0.15
alr 3841610 c.-190C>T upstream_gene_variant 0.11
rpoA 3878015 p.Asp165Tyr missense_variant 0.12
clpC1 4039553 c.1152C>A synonymous_variant 0.12
clpC1 4040294 p.Gln137His missense_variant 0.14
clpC1 4040481 p.Ser75Tyr missense_variant 0.11
clpC1 4040741 c.-37G>A upstream_gene_variant 0.18
embC 4242426 p.Arg855Leu missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4266956 c.1880delA frameshift_variant 0.11
ubiA 4269016 c.817delG frameshift_variant 0.12
aftB 4269768 c.-932C>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408113 c.89delG frameshift_variant 0.17