TB-Profiler result

Run: ERR751414
Summary

Run ID: ERR751414

Sample name:

Date: 02-04-2023 04:28:26

Number of reads: 4061930

Percentage reads mapped: 66.78

Strain: lineage4

Drug-resistance: MDR-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
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
rpoB 761140 p.His445Pro missense_variant 1.0 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 1.0 clofazimine, bedaquiline
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326505 c.966_968dupGAC disruptive_inframe_insertion 0.93 ethionamide
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
mshA 575837 c.490C>T synonymous_variant 1.0
rpoB 761889 p.Val695Leu missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777875 c.605delG frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.35
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.35
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.26
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.26
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.26
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.24
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.25
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.16
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.37
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.36
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.33
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.35
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.69
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.69
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.69
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.69
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.35
rrs 1472912 n.1067C>T non_coding_transcript_exon_variant 0.46
rrs 1472917 n.1072G>A non_coding_transcript_exon_variant 0.42
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.55
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.54
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.54
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.54
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.6
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.59
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.4
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.24
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.26
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.36
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.36
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.37
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.41
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.43
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.44
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.43
rrl 1475532 n.1875A>C non_coding_transcript_exon_variant 0.13
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.12
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.13
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.14
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.14
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.15
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.12
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.11
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.11
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.18
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.18
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.3
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.56
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.63
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.63
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.62
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.63
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.63
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.65
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.64
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.65
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.66
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.74
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.78
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.8
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.81
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.78
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.78
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.71
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.72
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.71
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.71
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.42
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.28
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101831 c.1212G>A synonymous_variant 0.99
katG 2156173 c.-62C>A upstream_gene_variant 1.0
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726141 c.-52C>A upstream_gene_variant 0.99
Rv2752c 3065517 c.675C>T synonymous_variant 1.0
thyA 3074495 c.-24C>T upstream_gene_variant 1.0
fprA 3474299 p.Asp98Gly missense_variant 1.0
Rv3236c 3612219 p.Val300Ile missense_variant 1.0
rpoA 3878595 c.-88C>T upstream_gene_variant 0.33
rpoA 3878635 c.-128C>T upstream_gene_variant 0.4
clpC1 4038857 c.1848C>A synonymous_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407967 p.Leu79Trp missense_variant 1.0