TB-Profiler result

Run: ERR245719
Summary

Run ID: ERR245719

Sample name:

Date: 31-03-2023 18:17:14

Number of reads: 13117605

Percentage reads mapped: 99.63

Strain: lineage4.9.1

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
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
lineage4.9.1 Euro-American (H37Rv-like) T1 None 0.96
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 5347 c.108G>C synonymous_variant 0.16
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.25
gyrA 8978 c.1677C>T synonymous_variant 0.97
mshA 575309 c.-39C>G upstream_gene_variant 0.18
rpoB 759831 p.Thr9Pro missense_variant 0.21
rpoB 762249 p.Leu815Val missense_variant 0.21
rpoC 762836 c.-534C>G upstream_gene_variant 0.29
rpoC 764725 p.Phe452Leu missense_variant 0.2
rpoC 767305 p.Tyr1312* stop_gained 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.15
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.21
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.27
Rv1979c 2223145 p.Arg7Lys missense_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289138 p.Leu35Arg missense_variant 0.99
pncA 2289448 c.-207G>A upstream_gene_variant 0.97
eis 2714569 p.Ala255Gly missense_variant 0.16
eis 2715586 c.-254G>C upstream_gene_variant 0.25
ahpC 2725954 c.-239C>T upstream_gene_variant 0.33
ahpC 2726550 p.Gln120Lys missense_variant 0.17
folC 2746186 c.1413G>C synonymous_variant 0.21
pepQ 2859680 p.Leu247Val missense_variant 0.18
Rv2752c 3064741 p.Gly484Ala missense_variant 0.21
Rv2752c 3067191 c.-1000G>A upstream_gene_variant 0.97
thyA 3073817 p.Gln219Glu missense_variant 0.32
fbiD 3339385 p.Asp90Asn missense_variant 0.98
Rv3083 3449673 p.Tyr390* stop_gained 0.22
Rv3236c 3611982 p.Ala379Pro missense_variant 0.31
fbiB 3641955 p.Gly141Arg missense_variant 0.24
alr 3841504 c.-84C>G upstream_gene_variant 0.2
clpC1 4039932 p.Gly258Val missense_variant 0.21
embC 4241056 c.1194C>G synonymous_variant 0.23
embC 4241128 c.1266G>C synonymous_variant 0.18
embC 4241456 p.Ala532Pro missense_variant 0.26
embC 4242476 p.Pro872Ala missense_variant 0.2
embC 4242822 p.Val987Gly missense_variant 0.27
embA 4244375 c.1143C>G synonymous_variant 0.28
ubiA 4269529 p.Ala102Gly missense_variant 0.25
ethA 4327672 c.-199G>A upstream_gene_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0