TB-Profiler result

Run: ERR2027285
Summary

Run ID: ERR2027285

Sample name:

Date: 31-03-2023 15:42:05

Number of reads: 2084995

Percentage reads mapped: 98.79

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 761139 p.His445Cys missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.54 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4327404 p.Gln24* stop_gained 1.0 ethionamide
gid 4408087 c.115delC frameshift_variant 1.0 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
rpoB 759615 c.-192A>C upstream_gene_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.15
rrs 1472354 n.509C>A non_coding_transcript_exon_variant 0.13
rrs 1472356 n.511A>C non_coding_transcript_exon_variant 0.13
rrs 1472364 n.519C>G non_coding_transcript_exon_variant 0.14
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.2
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.25
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.25
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.33
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.33
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.4
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.44
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.38
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.36
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.36
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.4
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.38
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.45
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.45
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.45
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.45
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.45
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.45
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.45
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.45
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.45
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.47
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.47
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.47
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.47
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.26
rrs 1472891 n.1047delT non_coding_transcript_exon_variant 0.13
rrl 1474067 n.410G>C non_coding_transcript_exon_variant 0.13
rrl 1474467 n.811delG non_coding_transcript_exon_variant 0.33
rrl 1474476 n.819C>G non_coding_transcript_exon_variant 0.4
rrl 1474479 n.822A>C non_coding_transcript_exon_variant 0.4
rrl 1474483 n.826C>G non_coding_transcript_exon_variant 0.4
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.4
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.5
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.67
rrl 1474529 n.872A>G non_coding_transcript_exon_variant 0.67
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.67
rrl 1474540 n.883T>C non_coding_transcript_exon_variant 0.67
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.67
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 1.0
rrl 1474555 n.898T>G non_coding_transcript_exon_variant 1.0
rrl 1474558 n.901G>C non_coding_transcript_exon_variant 1.0
rrl 1474581 n.924C>T non_coding_transcript_exon_variant 1.0
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.5
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.33
rrl 1474773 n.1116C>A non_coding_transcript_exon_variant 0.18
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.18
rrl 1474783 n.1126G>T non_coding_transcript_exon_variant 0.18
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.22
rrl 1474794 n.1137C>G non_coding_transcript_exon_variant 0.22
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.22
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.18
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.18
rrl 1474852 n.1195T>C non_coding_transcript_exon_variant 0.14
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.11
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.11
rrl 1474890 n.1233C>A non_coding_transcript_exon_variant 0.11
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.11
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.11
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.11
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.12
rrl 1474938 n.1281G>A non_coding_transcript_exon_variant 0.12
rrl 1474977 n.1320T>C non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.4
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.4
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.4
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.29
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.29
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.29
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.29
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.25
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.25
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.29
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.29
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
clpC1 4040469 p.Pro79Gln missense_variant 1.0
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0