TB-Profiler result

Run: ERR037547
Summary

Run ID: ERR037547

Sample name:

Date: 31-03-2023 08:36:55

Number of reads: 19657066

Percentage reads mapped: 99.39

Strain: lineage4.3.4.1;lineage1.1.3.2

Drug-resistance: Sensitive

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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 0.9
lineage4.3 Euro-American (LAM) mainly-LAM None 0.93
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.07
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.12
lineage4.3.4 Euro-American (LAM) LAM RD174 0.91
lineage1.1.3.2 Indo-Oceanic NA RD239 0.09
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.9
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
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 6112 p.Met291Ile missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619695 c.-196G>A upstream_gene_variant 0.11
rpoC 762836 c.-534C>G upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.21
rplC 801166 p.Gly120Ser missense_variant 0.11
atpE 1461019 c.-26C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.18
inhA 1674892 p.Asn231Asp missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.13
PPE35 2167983 p.Gly877Asp missense_variant 0.13
PPE35 2169320 p.Leu431Phe missense_variant 0.16
PPE35 2169866 c.747G>C synonymous_variant 0.32
Rv1979c 2222308 p.Asp286Gly missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.23
eis 2715586 c.-254G>C upstream_gene_variant 0.36
pepQ 2859381 c.1038C>G synonymous_variant 0.2
Rv2752c 3064552 p.Arg547Pro missense_variant 0.21
Rv2752c 3064741 p.Gly484Ala missense_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.15
Rv3236c 3612009 p.Ala370Thr missense_variant 0.91
fbiB 3640614 c.-921C>T upstream_gene_variant 0.93
fbiB 3641955 p.Gly141Arg missense_variant 0.22
fbiB 3642734 c.1200G>C synonymous_variant 0.17
rpoA 3878238 p.Asp90Glu missense_variant 0.16
ddn 3987013 p.Gly57Ala missense_variant 0.24
clpC1 4038287 c.2418C>T synonymous_variant 0.88
clpC1 4038857 c.1848C>A synonymous_variant 0.18
clpC1 4039932 p.Gly258Val missense_variant 0.27
clpC1 4040517 p.Val63Ala missense_variant 0.12
embC 4239842 c.-21C>A upstream_gene_variant 0.19
embC 4240671 p.Thr270Ile missense_variant 0.14
embC 4242476 p.Pro872Ala missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.44
embC 4242827 p.Leu989Val missense_variant 0.21
embA 4245329 c.2097A>G synonymous_variant 0.91
aftB 4269411 c.-575T>C upstream_gene_variant 0.92
ubiA 4269529 p.Ala102Gly missense_variant 0.16
ethA 4327672 c.-199G>A upstream_gene_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4407780 c.423G>A synonymous_variant 0.13
gid 4407873 c.330G>T synonymous_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 0.9