TB-Profiler result

Run: ERR025425
Summary

Run ID: ERR025425

Sample name:

Date: 31-03-2023 08:16:22

Number of reads: 696972

Percentage reads mapped: 99.06

Strain: lineage4.1.2

Drug-resistance: Other

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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 0.28
lineage4.1.2 Euro-American T;H None 0.39
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.31 streptomycin
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 6922 c.-380G>T upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8445 p.Arg382Gly missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.47
mshA 575679 p.Asn111Ser missense_variant 0.25
mshA 576077 c.730C>T synonymous_variant 0.68
mshA 576448 c.1101A>G synonymous_variant 0.2
mshA 576459 p.Ala371Val missense_variant 0.17
ccsA 619831 c.-60T>G upstream_gene_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 0.42
rpoC 765150 p.Gly594Glu missense_variant 0.58
rpoC 767314 p.Tyr1315* stop_gained 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777215 c.1266C>A synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417501 c.-154A>C upstream_gene_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474007 n.350A>C non_coding_transcript_exon_variant 0.33
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.2
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.21
fabG1 1673449 p.Thr4Pro missense_variant 0.36
rpsA 1833958 p.Ile139Met missense_variant 0.33
rpsA 1834441 p.Lys300Asn missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918377 c.438T>G synonymous_variant 0.22
Rv1979c 2221777 p.Ala463Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.23
eis 2714569 p.Ala255Gly missense_variant 0.27
Rv2752c 3064552 p.Arg547Pro missense_variant 0.33
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.5
thyA 3074654 c.-183T>G upstream_gene_variant 0.38
ald 3086742 c.-78A>C upstream_gene_variant 0.61
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449925 c.1422C>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.14
fbiB 3642786 p.Trp418Gly missense_variant 0.2
clpC1 4038857 c.1848C>A synonymous_variant 0.33
clpC1 4039932 p.Gly258Val missense_variant 0.42
embC 4241429 p.Phe523Val missense_variant 0.27
embC 4242476 p.Pro872Ala missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.27
embC 4242822 p.Val987Gly missense_variant 0.27
embB 4246941 p.Pro143Leu missense_variant 0.4
embB 4247603 p.Leu364Val missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0