TB-Profiler result

Run: ERR1873459
Summary

Run ID: ERR1873459

Sample name:

Date: 15-08-2022 11:09:26

Number of reads: 2213859

Percentage reads mapped: 79.59

Strain: lineage4.4.1.1

Drug-resistance: Pre-XDR-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 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
gyrA 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.98 kanamycin
embB 4248003 p.Gln497Arg missense_variant 0.98 ethambutol
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 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764936 p.Gln523Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.1
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.11
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.12
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.11
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.11
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.1
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.1
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.14
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.14
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.12
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.11
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.15
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.15
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.15
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.15
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.15
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.16
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.15
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.1
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.11
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.11
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.12
rrl 1475954 n.2297A>C non_coding_transcript_exon_variant 0.98
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.17
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.17
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.17
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.19
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.21
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.26
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.22
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.21
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.33
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.31
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.32
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.26
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.23
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.23
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.19
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.19
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rpsA 1833585 p.Asp15Gly missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.15
Rv2752c 3065039 p.Tyr385Asp missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.39
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339153 p.Leu12Phe missense_variant 0.17
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.19
clpC1 4038857 c.1848C>A synonymous_variant 0.26
embC 4239842 c.-21C>A upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407790 p.Ala138Glu missense_variant 1.0