TB-Profiler result

Run: ERR245848
Summary

Run ID: ERR245848

Sample name:

Date: 31-03-2023 18:24:48

Number of reads: 9875211

Percentage reads mapped: 92.35

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575309 c.-39C>G upstream_gene_variant 0.19
ccsA 620407 p.Pro173Ala missense_variant 0.25
rpoB 762249 p.Leu815Val missense_variant 0.16
rpoC 762836 c.-534C>G upstream_gene_variant 0.3
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417501 c.-154A>C upstream_gene_variant 0.3
atpE 1461019 c.-26C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.11
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.12
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.11
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.1
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.28
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.29
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.29
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.26
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.22
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.18
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.1
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.16
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.19
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.11
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.12
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.12
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.12
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.25
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.1
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.1
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.17
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.18
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.23
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.23
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.3
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.45
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.42
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.39
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.24
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.22
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.18
fabG1 1673449 p.Thr4Pro missense_variant 0.41
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.38
PPE35 2170156 p.Ala153Pro missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.27
eis 2715586 c.-254G>C upstream_gene_variant 0.73
ahpC 2725954 c.-239C>T upstream_gene_variant 0.32
ahpC 2726756 c.564C>G synonymous_variant 0.25
pepQ 2859381 c.1038C>G synonymous_variant 0.19
Rv2752c 3064741 p.Gly484Ala missense_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.3
Rv3236c 3611992 c.1125T>G synonymous_variant 0.48
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.17
fbiB 3642734 c.1200G>C synonymous_variant 0.24
alr 3840719 c.702A>G synonymous_variant 1.0
ddn 3987013 p.Gly57Ala missense_variant 0.21
clpC1 4038287 c.2418C>T synonymous_variant 0.99
clpC1 4038857 c.1848C>A synonymous_variant 0.17
clpC1 4039363 p.Ala448Pro missense_variant 0.25
clpC1 4039932 p.Gly258Val missense_variant 0.29
embC 4241128 c.1266G>C synonymous_variant 0.26
embC 4241429 p.Phe523Val missense_variant 0.44
embC 4241456 p.Ala532Pro missense_variant 0.35
embC 4242425 p.Arg855Gly missense_variant 0.2
embC 4242476 p.Pro872Ala missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.49
embC 4242827 p.Leu989Val missense_variant 0.25
embA 4243977 p.Ala249Pro missense_variant 0.33
ubiA 4269529 p.Ala102Gly missense_variant 0.15
ethA 4327672 c.-199G>A upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0