TB-Profiler result

Run: ERR4815488
Summary

Run ID: ERR4815488

Sample name:

Date: 01-04-2023 13:53:30

Number of reads: 168670

Percentage reads mapped: 58.24

Strain: lineage4.4.1

Drug-resistance: HR-TB

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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
lineage4.4 Euro-American S;T None 0.07
lineage4.4.1 Euro-American (S-type) S;T None 0.12
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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.5 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 7004 p.Gly589Arg missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7445 c.144C>A synonymous_variant 0.5
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762678 p.Leu958Ile missense_variant 0.5
rpoC 766245 p.Gln959Pro missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304192 p.Ala421Glu missense_variant 0.2
fbiC 1304206 p.Arg426Gly missense_variant 0.22
Rv1258c 1406973 p.Ala123Asp missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.33
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.67
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.33
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.33
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.67
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.33
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.33
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.5
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.67
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.67
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.67
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.67
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.67
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.67
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.67
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.67
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.67
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.5
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.29
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.29
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.67
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.67
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.67
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.67
rrs 1473150 n.1305T>C non_coding_transcript_exon_variant 0.33
rrs 1473161 n.1316A>G non_coding_transcript_exon_variant 0.4
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.5
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.5
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.5
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.6
rrs 1473201 n.1356A>G non_coding_transcript_exon_variant 0.4
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.4
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.6
rrs 1473215 n.1370A>G non_coding_transcript_exon_variant 0.6
rrl 1474495 n.838G>T non_coding_transcript_exon_variant 0.25
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.2
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.2
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.2
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.22
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.22
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.22
rrl 1474581 n.924C>T non_coding_transcript_exon_variant 0.5
rrl 1475713 n.2056C>T non_coding_transcript_exon_variant 0.4
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.5
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.67
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.62
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.22
rrl 1475772 n.2115A>C non_coding_transcript_exon_variant 0.67
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.67
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155950 c.162C>T synonymous_variant 0.29
PPE35 2168853 p.Pro587Leu missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223054 c.111T>G synonymous_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289748 c.-507C>A upstream_gene_variant 0.4
ahpC 2725945 c.-248G>T upstream_gene_variant 0.22
pepQ 2859921 c.498C>T synonymous_variant 0.67
pepQ 2860044 c.375C>G synonymous_variant 0.67
ribD 2986995 p.Ala53Thr missense_variant 0.4
thyA 3074271 c.201C>T synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3449645 p.Ala381Asp missense_variant 0.4
fbiB 3641691 p.Val53Leu missense_variant 0.25
alr 3841060 p.Gly121Arg missense_variant 0.4
alr 3841512 c.-92C>A upstream_gene_variant 0.33
ddn 3987262 p.Thr140Asn missense_variant 0.25
clpC1 4038635 p.Tyr690* stop_gained 0.67
clpC1 4040522 c.183T>C synonymous_variant 1.0
embC 4239819 c.-44G>A upstream_gene_variant 0.67
embA 4242391 c.-842G>A upstream_gene_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242825 p.Gly988Val missense_variant 0.5
embA 4243309 p.Leu26Pro missense_variant 0.29
embA 4245160 p.Ser643Ile missense_variant 0.22
embA 4245804 p.Gln858Lys missense_variant 0.67
aftB 4268158 p.Phe227Leu missense_variant 0.4
ubiA 4269169 p.Trp222* stop_gained 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0