TB-Profiler result

Run: SRR4033677
Summary

Run ID: SRR4033677

Sample name:

Date: 04-04-2023 06:14:54

Number of reads: 1099535

Percentage reads mapped: 99.76

Strain: lineage4.4.1.1.1

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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 Euro-American S;Orphans 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
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7673 c.372G>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762109 p.Pro768Gln missense_variant 0.13
rpoB 762372 p.Pro856Ser missense_variant 0.17
rpoC 762956 c.-414G>A upstream_gene_variant 0.15
rpoC 763641 p.Arg91Leu missense_variant 0.18
rpoC 765331 p.Ser654Arg missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776608 p.Gln625* stop_gained 0.15
mmpL5 776868 p.Arg538Gln missense_variant 0.14
mmpL5 777855 p.Ala209Val missense_variant 0.17
mmpS5 778829 p.Gln26Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781532 c.-28G>T upstream_gene_variant 0.29
fbiC 1303508 c.581delG frameshift_variant 0.1
embR 1416947 p.Ala134Val missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471857 n.12G>C non_coding_transcript_exon_variant 0.15
rrl 1475259 n.1602T>C non_coding_transcript_exon_variant 0.29
rpsA 1834872 p.Gly444Asp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101962 p.Pro361Ser missense_variant 0.11
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154732 c.1380C>T synonymous_variant 0.22
PPE35 2169320 p.Leu431Phe missense_variant 0.25
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170059 p.Val185Ala missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726292 p.Tyr34His missense_variant 0.11
ahpC 2726338 p.Val49Gly missense_variant 0.33
ahpC 2726599 p.Phe136Ser missense_variant 0.12
Rv2752c 3064662 c.1529delA frameshift_variant 0.22
Rv2752c 3067059 c.-869dupC upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086909 c.90C>T synonymous_variant 0.12
Rv3083 3448466 c.-38G>A upstream_gene_variant 0.12
Rv3083 3448504 c.1A>G start_lost 0.18
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474110 p.Ala35Asp missense_variant 0.15
fprA 3474527 p.Ala174Glu missense_variant 0.11
Rv3236c 3612112 p.Glu335Asp missense_variant 0.14
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3612766 c.351C>A synonymous_variant 0.12
fbiB 3642302 c.768C>A synonymous_variant 0.18
rpoA 3878036 p.Glu158Lys missense_variant 0.14
embC 4240186 c.324G>T synonymous_variant 0.12
embC 4241739 p.Val626Ala missense_variant 0.11
embC 4242390 p.Leu843Gln missense_variant 0.25
embC 4242425 p.Arg855Gly missense_variant 0.29
embA 4242445 c.-788C>A upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249496 p.Pro995Ala missense_variant 0.15
aftB 4267433 c.1404C>A synonymous_variant 0.18
aftB 4267475 c.1362G>T synonymous_variant 0.12
ethR 4327465 c.-84C>T upstream_gene_variant 0.13
ethR 4327700 p.Ala51Val missense_variant 0.12
ethA 4328133 c.-660C>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0