TB-Profiler result

Run: ERR4819347
Summary

Run ID: ERR4819347

Sample name:

Date: 01-04-2023 16:03:34

Number of reads: 1217310

Percentage reads mapped: 93.17

Strain: lineage4.1.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.88 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576590 c.1243C>A synonymous_variant 0.13
ccsA 619733 c.-158G>A upstream_gene_variant 0.15
ccsA 620008 p.Arg40Cys missense_variant 0.2
ccsA 620748 c.858T>G synonymous_variant 0.27
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761168 c.1362C>T synonymous_variant 0.12
rpoC 764302 c.933C>A synonymous_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304505 c.1575G>A synonymous_variant 0.11
fbiC 1305389 p.Ala820Gly missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.89
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.88
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.88
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.88
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.88
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.88
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.88
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.88
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.78
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.78
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.8
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.85
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.85
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.88
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.88
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.78
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.83
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.67
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.5
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.4
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.4
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 1.0
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 1.0
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 1.0
rrl 1473761 n.104T>A non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
inhA 1674075 c.-127C>T upstream_gene_variant 0.12
inhA 1674889 c.690delG frameshift_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918616 p.Lys226Met missense_variant 0.2
tlyA 1918688 p.Ala250Val missense_variant 0.22
katG 2155720 p.Pro131Gln missense_variant 0.13
PPE35 2170147 p.Ser156Ala missense_variant 0.17
PPE35 2170157 p.Ala152Ser missense_variant 0.18
PPE35 2170357 p.Ala86Thr missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518944 c.832delG frameshift_variant 0.14
eis 2714962 p.Gly124Asp missense_variant 0.12
folC 2746498 c.1101G>A synonymous_variant 0.12
pepQ 2859607 p.Arg271Leu missense_variant 0.18
pepQ 2860052 p.Arg123Trp missense_variant 0.12
pepQ 2860236 c.183C>A synonymous_variant 0.12
thyA 3074030 p.Ala148Thr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641878 p.Arg115Leu missense_variant 0.11
fbiB 3642294 p.Gln254* stop_gained 0.12
panD 4043993 p.Arg97Trp missense_variant 1.0
embA 4242568 c.-665C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244000 c.768G>T synonymous_variant 0.11
embA 4244061 p.Leu277Ile missense_variant 0.11
embA 4244184 p.Ser318Leu missense_variant 0.12
aftB 4267574 c.1263G>A synonymous_variant 0.12
aftB 4267595 c.1242C>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338598 c.-77G>A upstream_gene_variant 1.0