TB-Profiler result

Run: ERR2653042
Summary

Run ID: ERR2653042

Sample name:

Date: 31-03-2023 22:27:54

Number of reads: 1215004

Percentage reads mapped: 99.44

Strain: lineage4.1.1

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 0.98
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
rpsL 781821 p.Lys88Gln missense_variant 0.97 streptomycin
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 9304 p.Gly668Asp missense_variant 1.0
rpoC 763606 c.237C>A synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777192 p.Gly430Val missense_variant 0.15
mmpR5 778133 c.-857C>T upstream_gene_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781649 c.90T>C synonymous_variant 0.12
rplC 801272 p.Ala155Val missense_variant 0.15
Rv1258c 1406359 p.Ile328Phe missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475122 n.1465C>T non_coding_transcript_exon_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102712 p.Pro111Ser missense_variant 0.12
katG 2154083 p.Thr677Ala missense_variant 0.1
PPE35 2168026 p.Ala863Thr missense_variant 0.11
PPE35 2169013 p.Val534Leu missense_variant 0.33
PPE35 2169017 p.Leu532Phe missense_variant 0.25
PPE35 2170605 p.Tyr3Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289666 c.-425C>T upstream_gene_variant 0.11
eis 2714662 p.Ala224Val missense_variant 0.15
eis 2715287 p.Met16Val missense_variant 0.12
ahpC 2726210 c.18T>C synonymous_variant 0.97
Rv2752c 3064643 p.Ser517Thr missense_variant 0.11
Rv2752c 3065349 c.843G>T synonymous_variant 0.12
Rv2752c 3066004 p.Asp63Val missense_variant 0.11
Rv2752c 3066027 c.165C>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 0.97
Rv3083 3449403 c.903delC frameshift_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568617 p.His21Gln missense_variant 0.11
fbiA 3640679 p.Asn46Ser missense_variant 0.13
fbiA 3641447 p.Thr302Met missense_variant 0.96
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3878431 p.Leu26Pro missense_variant 0.11
rpoA 3878601 c.-95delG upstream_gene_variant 0.33
rpoA 3878630 c.-123G>C upstream_gene_variant 0.18
rpoA 3878637 c.-130G>C upstream_gene_variant 0.12
clpC1 4039939 p.Val256Leu missense_variant 0.13
embC 4240327 c.465G>A synonymous_variant 0.11
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243020 p.Trp1053Ser missense_variant 0.12
embA 4243484 c.252C>G synonymous_variant 0.95
embB 4246838 p.Ala109Ser missense_variant 1.0
embB 4247228 p.Leu239Val missense_variant 0.15
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338436 p.Val29Ala missense_variant 0.1
whiB6 4338498 p.Glu8Asp missense_variant 0.94
whiB6 4338595 c.-75delG upstream_gene_variant 1.0