TB-Profiler result

Run: SRR1640714

Summary

Run ID: SRR1640714

Sample name:

Date: 03-04-2023 17:41:47

Number of reads: 567910

Percentage reads mapped: 99.41

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 1.0
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
ethA 4326592 p.Cys294* stop_gained 0.12 ethionamide
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 5849 p.Leu204Met missense_variant 0.15
gyrB 5876 p.Val213Met 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 575850 p.Arg168Leu missense_variant 0.15
mshA 576475 c.1128G>T synonymous_variant 0.14
mshA 576586 c.1239G>T synonymous_variant 0.17
ccsA 619807 c.-84G>T upstream_gene_variant 0.12
ccsA 620106 c.216C>T synonymous_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 763467 p.Thr33Met missense_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766751 p.Arg1128Ser missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801379 p.Val191Leu missense_variant 0.12
Rv1258c 1406935 p.Gly136Cys missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473750 n.93C>A non_coding_transcript_exon_variant 0.12
rrl 1476010 n.2353G>T non_coding_transcript_exon_variant 0.13
rrl 1476631 n.2974G>A non_coding_transcript_exon_variant 0.74
inhA 1674416 p.Ala72Asp missense_variant 0.12
inhA 1674453 c.252G>T synonymous_variant 0.12
tlyA 1917919 c.-21C>A upstream_gene_variant 0.17
tlyA 1917967 p.Glu10* stop_gained 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156072 p.Gly14Arg missense_variant 0.12
PPE35 2169775 p.Ala280Thr missense_variant 1.0
PPE35 2169824 c.789C>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746665 p.Phe312Leu missense_variant 0.13
folC 2747019 p.Ile194Val missense_variant 0.11
pepQ 2859941 p.Arg160Cys missense_variant 0.13
pepQ 2860263 c.156C>T synonymous_variant 0.12
Rv2752c 3064595 p.Val533Met missense_variant 1.0
Rv2752c 3064750 p.Arg481Leu missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087656 c.837A>G synonymous_variant 0.1
fbiD 3339721 p.Gly202Trp missense_variant 0.14
Rv3083 3449205 c.702G>T synonymous_variant 0.14
Rv3083 3449277 p.Cys258* stop_gained 0.13
Rv3083 3449366 p.Pro288Gln missense_variant 0.17
Rv3083 3449566 p.Gly355Arg missense_variant 1.0
Rv3083 3449848 p.Asp449Tyr missense_variant 0.13
Rv3083 3449865 p.Gln454His missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475284 c.1278C>T synonymous_variant 0.13
fbiA 3640711 p.Arg57Cys missense_variant 0.12
fbiA 3640812 p.Gln90His missense_variant 0.13
fbiA 3640836 p.Gln98His missense_variant 0.12
fbiA 3640885 p.Arg115Cys missense_variant 0.12
fbiA 3641406 p.Trp288Cys missense_variant 0.12
fbiB 3641738 p.Glu68Asp missense_variant 0.14
alr 3841364 c.56delG frameshift_variant 0.1
ddn 3986762 c.-82G>C upstream_gene_variant 0.1
clpC1 4039321 p.Ala462Ser missense_variant 0.13
clpC1 4040680 p.Ala9Ser missense_variant 0.12
clpC1 4040760 c.-56C>A upstream_gene_variant 0.13
embC 4241196 p.Ser445Leu missense_variant 0.17
embC 4241753 p.Ala631Ser missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243764 p.Lys178* stop_gained 0.14
embA 4243820 c.588C>A synonymous_variant 0.17
embA 4243898 c.666C>A synonymous_variant 0.12
embA 4244281 p.Gly350Val missense_variant 0.15
embB 4247038 c.525C>A synonymous_variant 0.14
embB 4249380 p.Thr956Ile missense_variant 0.74
ethA 4326779 p.Thr232Ile missense_variant 0.15
ethA 4327728 c.-255C>T upstream_gene_variant 1.0
whiB6 4338449 p.Ala25Ser missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0