TB-Profiler result

Run: ERR245823
Summary

Run ID: ERR245823

Sample name:

Date: 31-03-2023 18:23:01

Number of reads: 1748437

Percentage reads mapped: 99.24

Strain: lineage4.1.1.3

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 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 5347 c.108G>C synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8445 p.Arg382Gly missense_variant 0.23
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9585 p.Leu762Val missense_variant 0.38
rpoB 759620 c.-187A>C upstream_gene_variant 0.17
rpoC 762836 c.-534C>G upstream_gene_variant 0.75
rpoC 764725 p.Phe452Leu missense_variant 0.47
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766535 p.Glu1056Gln missense_variant 0.18
rpoC 766628 p.Arg1087Gly missense_variant 0.28
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.2
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.21
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.22
fabG1 1673449 p.Thr4Pro missense_variant 0.25
inhA 1674892 p.Asn231Asp missense_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918237 p.Leu100Val missense_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.15
PPE35 2169866 c.747G>C synonymous_variant 0.63
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519142 p.Leu343Arg missense_variant 0.11
eis 2714366 p.Val323Leu missense_variant 0.4
ahpC 2725954 c.-239C>T upstream_gene_variant 0.27
ahpC 2726756 c.564C>G synonymous_variant 0.31
folC 2746186 c.1413G>C synonymous_variant 0.33
pepQ 2859381 c.1038C>G synonymous_variant 0.25
pepQ 2859680 p.Leu247Val missense_variant 0.31
Rv2752c 3064552 p.Arg547Pro missense_variant 0.33
Rv2752c 3064741 p.Gly484Ala missense_variant 0.29
thyA 3073817 p.Gln219Glu missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448929 p.Tyr142* stop_gained 0.17
Rv3083 3449058 p.Ser185Arg missense_variant 0.42
Rv3083 3449673 p.Tyr390* stop_gained 0.38
Rv3083 3449731 p.Leu410Val missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612425 p.Ala231Gly missense_variant 0.4
fbiB 3641955 p.Gly141Arg missense_variant 0.29
alr 3841167 p.Gly85Val missense_variant 0.12
rpoA 3878638 c.-131C>T upstream_gene_variant 1.0
clpC1 4039363 p.Ala448Pro missense_variant 0.45
clpC1 4039932 p.Gly258Val missense_variant 0.44
embC 4239842 c.-21C>A upstream_gene_variant 0.2
embC 4240521 p.Thr220Asn missense_variant 0.5
embC 4241128 c.1266G>C synonymous_variant 0.3
embC 4241429 p.Phe523Val missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243287 p.Val19Ile missense_variant 1.0
embA 4244182 p.Val317Gly missense_variant 0.4
embA 4244374 p.Pro381Arg missense_variant 0.29
embA 4244460 p.Val410Leu missense_variant 0.25
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267156 p.Gln561Lys missense_variant 0.26
aftB 4267527 p.Ala437Gly missense_variant 0.25
ubiA 4269529 p.Ala102Gly missense_variant 0.22
ethA 4327672 c.-199G>A upstream_gene_variant 0.29
ethR 4327804 p.Ala86Ser missense_variant 0.25
ethR 4327912 p.Arg122Gly missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0