TB-Profiler result

Run: ERR4813243
Summary

Run ID: ERR4813243

Sample name:

Date: 01-04-2023 12:37:30

Number of reads: 795208

Percentage reads mapped: 99.65

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 1.0
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrB 5309 p.Glu24Lys missense_variant 0.12
gyrB 5314 c.75C>G synonymous_variant 0.12
gyrB 5862 p.Leu208Gln missense_variant 0.12
gyrB 6627 p.Ala463Gly missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491102 p.Thr107Ile missense_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.24
rpoB 759653 c.-154C>A upstream_gene_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760282 p.Thr159Lys missense_variant 0.2
rpoB 762684 p.Ala960Pro missense_variant 0.11
rpoB 763096 p.Tyr1097Cys missense_variant 0.11
rpoB 763109 c.3305delA frameshift_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767070 p.Thr1234Ser missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776335 p.Val716Met missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472699 n.854G>C non_coding_transcript_exon_variant 0.4
rrl 1474286 n.629C>T non_coding_transcript_exon_variant 0.4
rrl 1474672 n.1015C>A non_coding_transcript_exon_variant 0.25
rrl 1475807 n.2150A>G non_coding_transcript_exon_variant 0.29
rrl 1475904 n.2247G>A non_coding_transcript_exon_variant 0.29
fabG1 1673267 c.-173C>T upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102543 p.Arg167Leu missense_variant 0.12
ndh 2102846 p.Gly66Val missense_variant 0.18
katG 2156199 c.-88G>A upstream_gene_variant 0.14
katG 2156370 c.-259T>G upstream_gene_variant 1.0
PPE35 2167931 c.2682C>A synonymous_variant 0.13
PPE35 2169529 p.Leu362Val missense_variant 0.25
PPE35 2169894 p.Gly240Asp missense_variant 0.17
Rv1979c 2222169 c.996C>T synonymous_variant 0.12
Rv1979c 2222794 p.Asp124Gly missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715089 p.Leu82Ile missense_variant 0.14
Rv2752c 3064876 p.Ser439Tyr missense_variant 0.12
thyX 3067388 c.558C>A synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449127 c.624G>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640510 c.-33G>T upstream_gene_variant 0.15
clpC1 4038588 p.Arg706His missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244708 c.1476C>T synonymous_variant 0.15
ethA 4326232 c.1242T>C synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0