TB-Profiler result

Run: SRR20139561
Summary

Run ID: SRR20139561

Sample name:

Date: 03-04-2023 21:50:12

Number of reads: 1426078

Percentage reads mapped: 99.57

Strain: lineage4.1.2.1

Drug-resistance: RR-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 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
pncA 2289081 p.Pro54Gln missense_variant 1.0 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 1.0 ethambutol
gid 4407816 c.386delG frameshift_variant 1.0 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
gyrB 6913 p.Asn558Lys missense_variant 0.15
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 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576710 p.Arg455Gly missense_variant 0.15
mshA 576718 c.1371C>G synonymous_variant 0.16
mshA 576741 p.Ala465Gly missense_variant 0.17
ccsA 620561 p.Thr224Asn missense_variant 0.17
ccsA 620571 c.681A>G synonymous_variant 0.2
ccsA 620748 c.858T>G synonymous_variant 0.17
ccsA 620756 p.Asp289Gly missense_variant 0.18
ccsA 620773 p.Ile295Val missense_variant 0.16
rpoB 759611 c.-196G>C upstream_gene_variant 0.16
rpoB 759615 c.-192A>C upstream_gene_variant 0.22
rpoB 759620 c.-187A>C upstream_gene_variant 0.23
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762717 p.Phe971Leu missense_variant 0.56
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.22
fbiC 1304146 p.Ile406Val missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918164 c.225G>A synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.29
ndh 2103235 c.-193C>G upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.98
ahpC 2726338 p.Val49Gly missense_variant 0.21
ahpC 2726341 p.Val50Gly missense_variant 0.23
ahpC 2726350 p.Trp53Leu missense_variant 0.24
ribD 2987323 p.Val162Gly missense_variant 0.19
thyA 3074595 c.-124C>T upstream_gene_variant 0.23
thyA 3074601 c.-130T>G upstream_gene_variant 0.18
thyA 3074608 c.-137A>G upstream_gene_variant 0.23
thyA 3074633 c.-162C>G upstream_gene_variant 0.17
thyA 3074641 c.-170C>T upstream_gene_variant 0.25
thyA 3074645 c.-174T>G upstream_gene_variant 0.42
thyA 3074648 c.-177T>G upstream_gene_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038177 p.Pro843Arg missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4248441 p.Thr643Ile missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0