TB-Profiler result

Run: ERR4815555
Summary

Run ID: ERR4815555

Sample name:

Date: 01-04-2023 13:56:04

Number of reads: 4017108

Percentage reads mapped: 89.95

Strain: lineage4.1.2.1

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 0.98
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8588 c.1287G>A synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.91
mshA 575679 p.Asn111Ser missense_variant 0.96
rpoB 760115 c.309C>T synonymous_variant 0.97
rpoC 763456 c.87A>G synonymous_variant 0.14
rpoC 763486 c.117T>G synonymous_variant 0.14
rpoC 763853 p.Val162Ile missense_variant 0.13
rpoC 764236 c.867G>A synonymous_variant 0.12
rpoC 764650 c.1281G>C synonymous_variant 0.13
rpoC 764651 p.Ser428Thr missense_variant 0.13
rpoC 764764 c.1395T>C synonymous_variant 0.13
rpoC 764809 c.1440C>T synonymous_variant 0.16
rpoC 764815 c.1446A>G synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304808 c.1878C>G synonymous_variant 0.18
fbiC 1304811 c.1881C>G synonymous_variant 0.19
fbiC 1304817 c.1887T>C synonymous_variant 0.24
fbiC 1304829 c.1899T>C synonymous_variant 0.31
fbiC 1304832 c.1902C>T synonymous_variant 0.3
fbiC 1304856 c.1926C>G synonymous_variant 0.61
fbiC 1304862 c.1932G>A synonymous_variant 0.28
fbiC 1304869 c.1939C>T synonymous_variant 0.23
fbiC 1304875 p.Ile649Val missense_variant 0.2
fbiC 1304883 p.Glu651Asp missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.25
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.18
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.18
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.2
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.17
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.17
rrl 1474076 n.419C>A non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.13
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.12
rrl 1476707 n.3050C>T non_coding_transcript_exon_variant 1.0
inhA 1674888 c.687C>G synonymous_variant 0.14
inhA 1674903 c.702T>C synonymous_variant 0.15
inhA 1674904 p.Ala235Pro missense_variant 0.15
rpsA 1833971 c.430C>T synonymous_variant 0.14
rpsA 1833979 c.438T>C synonymous_variant 0.13
rpsA 1834000 c.459G>C synonymous_variant 0.15
rpsA 1834021 c.480C>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.99
thyX 3067850 c.96A>C synonymous_variant 0.12
thyA 3074205 p.Glu89Asp missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038749 c.1956C>G synonymous_variant 0.14
clpC1 4038755 c.1950G>T synonymous_variant 0.14
clpC1 4038770 c.1935C>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.95
embA 4245137 c.1905T>C synonymous_variant 0.14
embA 4245146 c.1914G>A synonymous_variant 0.14
embA 4245149 c.1917C>G synonymous_variant 0.16
embA 4245153 p.Ile641Val missense_variant 0.17
embA 4245182 c.1950T>C synonymous_variant 0.2
embA 4245189 c.1957C>T synonymous_variant 0.18
embA 4245198 p.Leu656Ile missense_variant 0.16
embA 4245207 c.1975T>C synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0