TB-Profiler result

Run: ERR4814939
Summary

Run ID: ERR4814939

Sample name:

Date: 01-04-2023 13:34:34

Number of reads: 1193575

Percentage reads mapped: 99.11

Strain: lineage4.3.3;lineage3

Drug-resistance: Other

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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
lineage3 East-African-Indian CAS RD750 0.15
lineage4 Euro-American LAM;T;S;X;H None 0.85
lineage4.3 Euro-American (LAM) mainly-LAM None 0.86
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.84
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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.6 streptomycin
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 8040 p.Gly247Ser missense_variant 0.78
gyrA 8808 p.Gly503Arg missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.97
fgd1 491742 c.960T>C synonymous_variant 0.1
rpoB 759746 c.-61C>T upstream_gene_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 0.19
rpoC 764995 c.1626C>G synonymous_variant 0.91
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.29
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.67
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.67
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.5
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.5
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.5
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.5
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.75
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.4
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.4
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.4
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.4
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.4
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.75
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.6
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.4
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.4
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.4
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.5
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.6
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.6
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.5
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.5
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.75
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.75
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.67
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.67
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.67
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.8
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.75
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.75
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.75
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.43
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.33
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.33
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.33
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.33
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.33
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.33
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.33
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.33
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.33
rrl 1473904 n.247G>A non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.33
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.33
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.33
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.29
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.25
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.25
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.44
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.57
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.62
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.43
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 0.19
PPE35 2169902 c.711G>C synonymous_variant 0.11
PPE35 2169910 p.Asn235Tyr missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.26
kasA 2518919 p.Gly269Ser missense_variant 0.76
ahpC 2726105 c.-88G>A upstream_gene_variant 0.24
Rv2752c 3066313 c.-122T>G upstream_gene_variant 0.8
thyA 3073868 p.Thr202Ala missense_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 0.71
embC 4241650 p.Leu596Phe missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 0.17
embC 4242182 p.Ala774Ser missense_variant 0.85
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244869 p.Ser546Ile missense_variant 0.12
embA 4245100 p.Gly623Ala missense_variant 0.86
aftB 4268537 c.300G>T synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.76