TB-Profiler result

Run: ERR2653041
Summary

Run ID: ERR2653041

Sample name:

Date: 31-03-2023 22:27:55

Number of reads: 1174481

Percentage reads mapped: 99.32

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 1.0
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 1.0 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
rpoB 763240 p.Glu1145Gly missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776800 p.Val561Met missense_variant 0.1
mmpL5 778125 p.Asp119Gly missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472556 n.711C>A non_coding_transcript_exon_variant 0.11
rrs 1473024 n.1179G>T non_coding_transcript_exon_variant 0.12
rrl 1475122 n.1465C>T non_coding_transcript_exon_variant 1.0
rrl 1475691 n.2034C>T non_coding_transcript_exon_variant 0.13
rpsA 1834541 p.Pro334Ser missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103012 p.Pro11Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714308 p.Pro342Gln missense_variant 0.11
eis 2714334 c.999C>A synonymous_variant 0.11
eis 2715309 c.23delC frameshift_variant 0.11
ahpC 2726210 c.18T>C synonymous_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339741 c.624G>C synonymous_variant 0.14
Rv3083 3448404 c.-99delG upstream_gene_variant 0.12
Rv3083 3448581 p.Glu26Asp missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568597 p.Trp28* stop_gained 0.12
fbiA 3641447 p.Thr302Met missense_variant 0.95
alr 3840285 p.Trp379* stop_gained 0.12
rpoA 3877553 p.Glu319Lys missense_variant 0.97
rpoA 3878567 c.-60C>G upstream_gene_variant 0.2
rpoA 3878599 c.-92C>G upstream_gene_variant 0.11
rpoA 3878601 c.-95delG upstream_gene_variant 0.24
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 0.18
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241150 p.Ile430Phe missense_variant 0.11
embC 4241439 p.Ser526Ile missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243484 c.252C>G synonymous_variant 0.95
embB 4246555 c.42G>C synonymous_variant 0.14
embB 4246556 p.Ala15Pro missense_variant 0.14
embB 4246563 p.Leu17Trp missense_variant 0.14
embB 4246567 c.54G>T synonymous_variant 0.17
embB 4246838 p.Ala109Ser missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269556 p.Ala93Asp missense_variant 0.11
whiB6 4338498 p.Glu8Asp missense_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 1.0