TB-Profiler result

Run: SRR4034222
Summary

Run ID: SRR4034222

Sample name:

Date: 04-04-2023 06:38:52

Number of reads: 663909

Percentage reads mapped: 99.58

Strain: lineage4.3.2.1

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 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
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 5247 p.Ala3Val missense_variant 0.12
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 6220 c.981G>T synonymous_variant 0.15
gyrB 6953 p.Lys572Glu missense_variant 0.12
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576258 p.Ser304Ile missense_variant 0.2
ccsA 620701 p.Ala271Thr missense_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765476 p.Arg703Cys missense_variant 0.14
rpoC 767066 p.Leu1233Val missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775831 p.Ala884Thr missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801390 c.582C>T synonymous_variant 0.22
fbiC 1304927 p.Gly666Asp missense_variant 0.2
Rv1258c 1406711 c.630C>T synonymous_variant 0.13
embR 1417490 c.-143C>T upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471898 n.57_58dupCA non_coding_transcript_exon_variant 0.18
rrs 1472199 n.354C>T non_coding_transcript_exon_variant 0.2
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1473136 n.1291A>G non_coding_transcript_exon_variant 0.12
rrl 1476429 n.2774delG non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168926 p.Val563Met missense_variant 0.13
PPE35 2169186 p.Ser476Asn missense_variant 0.17
PPE35 2169794 c.819C>A synonymous_variant 0.11
PPE35 2169798 c.814dupC frameshift_variant 0.12
Rv1979c 2222594 p.Asn191Asp missense_variant 0.12
Rv1979c 2223072 c.92delG frameshift_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518297 c.183C>A synonymous_variant 0.12
kasA 2519332 c.1218C>A synonymous_variant 0.22
ahpC 2726691 c.502dupC frameshift_variant 0.15
Rv2752c 3064900 p.Leu431Gln missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086886 p.Val23Ile missense_variant 0.17
Rv3083 3448571 p.Val23Ala missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568749 c.-71delC upstream_gene_variant 0.18
fbiB 3641157 c.-378C>T upstream_gene_variant 0.22
fbiA 3641461 p.Pro307Ser missense_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038335 c.2369delT frameshift_variant 0.25
clpC1 4040583 p.Gly41Val missense_variant 0.12
embC 4239716 c.-147G>T upstream_gene_variant 0.25
embC 4240693 c.831T>C synonymous_variant 1.0
embC 4242098 p.Gly746Ser missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244295 p.Ala355Ser missense_variant 0.5
embA 4245375 c.2146delT frameshift_variant 0.2
embA 4245425 c.2193C>T synonymous_variant 0.29
embB 4248564 p.Ala684Val missense_variant 0.17
embB 4249675 c.3162C>T synonymous_variant 0.25
aftB 4267661 c.1176G>A synonymous_variant 0.4
aftB 4268481 p.Pro119Leu missense_variant 0.15
aftB 4268558 c.279G>A synonymous_variant 0.12
ubiA 4269972 c.-139G>A upstream_gene_variant 0.15
ethA 4326391 c.1083G>A synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0