TB-Profiler result

Run: ERR2124090
Summary

Run ID: ERR2124090

Sample name:

Date: 31-03-2023 15:52:08

Number of reads: 4898646

Percentage reads mapped: 98.79

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.98
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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 761139 p.His445Asp missense_variant 0.98 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.18 streptomycin
katG 2155276 p.Gly279Asp missense_variant 0.98 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.97
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.98
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.98
mmpL5 776182 p.Asp767Asn missense_variant 0.95
mmpS5 779615 c.-710C>G upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.3
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.41
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.58
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.62
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.67
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.72
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.74
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.75
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.58
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.57
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.35
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.27
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.27
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.29
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.28
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.24
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.66
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.69
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.69
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.68
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.66
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.66
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.66
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.39
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.18
rrs 1472418 n.573T>C non_coding_transcript_exon_variant 0.15
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.15
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.11
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.14
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.3
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.46
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.44
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.43
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.45
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.81
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.83
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.86
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.84
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.57
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.57
rrs 1472836 n.991G>C non_coding_transcript_exon_variant 0.44
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.14
rrs 1472912 n.1067C>T non_coding_transcript_exon_variant 0.15
rrs 1472917 n.1072G>A non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.2
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.33
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.33
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.36
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.36
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.36
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.36
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.36
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.36
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.35
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.23
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.16
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.17
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.16
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.19
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.16
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.16
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.16
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.15
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.16
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.16
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.16
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.37
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.44
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.44
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.43
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.44
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.54
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.52
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.51
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.51
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.5
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.61
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.61
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.62
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.61
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.45
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.45
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.46
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.47
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.42
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.41
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.19
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.97
embB 4249757 p.Thr1082Ala missense_variant 0.99
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338501 c.21A>G synonymous_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.98
gid 4407927 p.Glu92Asp missense_variant 0.97