TB-Profiler result

Run: ERR4818322
Summary

Run ID: ERR4818322

Sample name:

Date: 01-04-2023 15:29:33

Number of reads: 346535

Percentage reads mapped: 89.95

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 0.96
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 0.86 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 576104 p.Arg253Ser missense_variant 0.25
rpoB 760072 p.Pro89Leu missense_variant 0.25
rpoB 760106 c.300G>A synonymous_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762477 p.Lys891Glu missense_variant 0.4
rpoB 762984 p.Gln1060* stop_gained 0.25
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767279 p.Ala1304Thr missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776585 c.1896C>T synonymous_variant 0.2
mmpL5 776688 p.Trp598* stop_gained 0.33
mmpL5 778299 p.Ala61Val missense_variant 0.18
mmpS5 779638 c.-733C>T upstream_gene_variant 0.2
mmpS5 779640 c.-735G>C upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781576 p.Gln6Arg missense_variant 0.14
fbiC 1303287 c.357C>T synonymous_variant 0.33
fbiC 1304531 p.Ser534Leu missense_variant 0.33
fbiC 1305025 p.Glu699Lys missense_variant 0.29
Rv1258c 1407137 p.Tyr68* stop_gained 0.2
embR 1416222 p.Phe376Leu missense_variant 0.29
embR 1416232 p.Cys372Gly missense_variant 0.22
embR 1416299 p.Val350Glu missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471850 n.5G>T non_coding_transcript_exon_variant 0.2
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_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 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.33
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 0.5
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.8
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.8
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 1472767 n.922G>A non_coding_transcript_exon_variant 0.22
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.78
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.75
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.75
rrs 1472983 n.1138A>G non_coding_transcript_exon_variant 0.67
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.22
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.57
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.22
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.22
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.44
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.5
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.5
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.57
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.5
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.5
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.5
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.67
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.8
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.8
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102089 c.954C>T synonymous_variant 0.5
ndh 2102602 p.Leu147Phe missense_variant 0.33
ndh 2103117 c.-75G>A upstream_gene_variant 0.29
PPE35 2169479 c.1134C>T synonymous_variant 0.33
PPE35 2169902 p.Leu237Phe missense_variant 0.67
PPE35 2169910 p.Asn235Tyr missense_variant 0.67
PPE35 2170213 p.Ala134Pro missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289341 c.-100G>T upstream_gene_variant 0.22
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714698 p.Arg212His missense_variant 0.4
ahpC 2726389 p.Ala66Val missense_variant 0.25
Rv2752c 3066150 c.42C>T synonymous_variant 0.25
Rv2752c 3066241 c.-50C>T upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339556 p.Gly147Ser missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642417 p.Thr295Ser missense_variant 0.2
alr 3840397 p.Cys342Ser missense_variant 0.18
alr 3841282 p.His47Asn missense_variant 0.15
panD 4044275 p.Arg3Trp missense_variant 0.33
embC 4240369 c.507C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243158 c.-75G>A upstream_gene_variant 0.25
embA 4243184 c.-49G>A upstream_gene_variant 0.18
embA 4244000 c.768G>T synonymous_variant 0.17
embB 4248846 c.2336delC frameshift_variant 0.25
aftB 4267094 c.1743G>A synonymous_variant 0.14
aftB 4267160 c.1677C>T synonymous_variant 0.11
aftB 4267782 c.1054delG frameshift_variant 0.2
aftB 4268035 p.Val268Leu missense_variant 0.25
aftB 4268871 c.-35G>T upstream_gene_variant 0.5
ethA 4327319 p.Gly52Glu missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0