TB-Profiler result

Run: ERR2652959
Summary

Run ID: ERR2652959

Sample name:

Date: 31-03-2023 22:25:09

Number of reads: 442183

Percentage reads mapped: 99.7

Strain: lineage4.4.1.1

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 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 0.99
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 5682 p.Gln148Arg missense_variant 0.1
gyrB 6077 p.Gly280Ser missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7887 p.Glu196Lys missense_variant 0.2
gyrA 8908 p.Ser536Asn missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620330 c.442delC frameshift_variant 0.18
ccsA 620535 p.Met215Ile missense_variant 0.15
rpoB 761752 p.Ala649Val missense_variant 0.14
rpoB 761998 p.Leu731Pro missense_variant 0.17
rpoC 763932 p.Gly188Asp missense_variant 0.12
rpoC 767040 p.Ala1224Val missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779236 p.Leu83Ile missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801113 p.Thr102Ile missense_variant 0.13
fbiC 1304906 p.Ala659Val missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473285 n.1443delC non_coding_transcript_exon_variant 0.17
rrs 1473317 n.1472G>A non_coding_transcript_exon_variant 0.15
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.12
rrl 1475355 n.1698C>A non_coding_transcript_exon_variant 0.11
rrl 1475905 n.2248G>A non_coding_transcript_exon_variant 0.12
rrl 1476442 n.2785T>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
ndh 2103030 p.Gln5* stop_gained 0.17
katG 2154396 c.1716G>A synonymous_variant 0.2
katG 2155484 p.Tyr210His missense_variant 0.22
katG 2155516 p.Gly199Asp missense_variant 0.17
PPE35 2167720 p.Ser965Gly missense_variant 0.11
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2222743 p.Phe141Ser missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715307 p.Thr9Asn missense_variant 0.15
ahpC 2726238 p.Thr16Ala missense_variant 0.14
folC 2747704 c.-106A>G upstream_gene_variant 0.17
pepQ 2859463 p.Gly319Asp missense_variant 0.18
ribD 2987411 c.573T>C synonymous_variant 0.22
Rv2752c 3065355 c.837A>G synonymous_variant 0.15
Rv2752c 3067187 c.-996C>T upstream_gene_variant 0.25
thyX 3067893 p.Leu18Ser missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612011 c.1096_1105delGGTCCGATAC frameshift_variant 0.12
Rv3236c 3612508 c.608delG frameshift_variant 0.22
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3877979 p.Lys177Glu missense_variant 0.22
ddn 3986691 c.-153G>T upstream_gene_variant 0.11
clpC1 4040632 p.His25Asn missense_variant 0.11
embC 4240713 p.Trp284* stop_gained 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268778 p.Gly20Glu missense_variant 0.18
aftB 4269666 c.-830G>A upstream_gene_variant 0.4
ethA 4326325 c.1149G>A synonymous_variant 1.0
ethA 4327313 p.Arg54His missense_variant 0.17
whiB6 4338258 c.264G>A synonymous_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0