TB-Profiler result

Run: SRR18213909
Summary

Run ID: SRR18213909

Sample name:

Date: 03-04-2023 19:34:02

Number of reads: 398173

Percentage reads mapped: 89.23

Strain: lineage4.1.2.1

Drug-resistance: Other

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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
ethA 4326026 c.1447delA frameshift_variant 0.13 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
gyrB 5702 p.Pro155Ser missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8269 c.970delG frameshift_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9569 c.2268C>T synonymous_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575423 p.Arg26Cys missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576347 p.Thr334Ala missense_variant 0.14
ccsA 620537 p.Val216Gly missense_variant 0.16
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760243 p.Val146Gly missense_variant 0.11
rpoB 761838 p.Ala678Thr missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765873 p.Pro835Leu missense_variant 0.11
rpoC 766746 c.3382delC frameshift_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776714 c.1766delA frameshift_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.33
fbiC 1303823 p.Lys298Arg missense_variant 0.18
Rv1258c 1407318 p.Pro8Gln missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472836 n.991G>A non_coding_transcript_exon_variant 1.0
rrs 1472840 n.995A>T non_coding_transcript_exon_variant 1.0
rrs 1472844 n.999C>T non_coding_transcript_exon_variant 1.0
rrs 1472845 n.1000G>C non_coding_transcript_exon_variant 1.0
rrs 1472846 n.1001C>G non_coding_transcript_exon_variant 1.0
rrs 1472848 n.1003T>G non_coding_transcript_exon_variant 1.0
rrs 1472859 n.1014G>T non_coding_transcript_exon_variant 1.0
rrs 1472861 n.1016G>T non_coding_transcript_exon_variant 1.0
rrs 1472866 n.1023dupT non_coding_transcript_exon_variant 1.0
rrs 1472874 n.1029C>T non_coding_transcript_exon_variant 1.0
rrs 1472875 n.1030T>G non_coding_transcript_exon_variant 1.0
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 1.0
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.33
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.33
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.5
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.4
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.4
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.33
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.4
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
fabG1 1674076 p.Thr213Pro missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167668 p.Phe982Ser missense_variant 0.17
PPE35 2168370 p.Ala748Val missense_variant 0.18
PPE35 2168844 p.Thr590Met missense_variant 0.22
Rv1979c 2222283 c.882C>G synonymous_variant 0.13
Rv1979c 2223014 p.Tyr51His missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.25
eis 2714341 p.Leu331Pro missense_variant 0.11
eis 2715227 p.Trp36Arg missense_variant 0.11
ahpC 2725977 c.-216C>G upstream_gene_variant 0.17
pepQ 2859331 p.Thr363Ile missense_variant 0.2
pepQ 2859416 p.Gly335Ser missense_variant 0.15
pepQ 2860500 c.-82C>A upstream_gene_variant 0.11
ribD 2987176 p.Glu113Gly missense_variant 0.11
Rv2752c 3065234 p.Arg320Cys missense_variant 0.17
thyX 3067241 c.705G>T synonymous_variant 0.2
thyX 3068046 c.-101G>A upstream_gene_variant 0.18
thyA 3074511 c.-40C>T upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339068 c.-50G>A upstream_gene_variant 0.15
Rv3083 3448563 c.60C>T synonymous_variant 0.22
Rv3083 3449981 p.Ala493Val missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840285 c.1135delT frameshift_variant 0.17
alr 3841225 p.Lys66Glu missense_variant 0.11
rpoA 3878064 c.443dupC frameshift_variant 0.18
ddn 3987241 p.Tyr133Ser missense_variant 0.17
embA 4242541 c.-692C>G upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243870 p.Ala213Val missense_variant 0.18
embB 4249018 p.Tyr835* stop_gained 0.17
embB 4249361 p.Ala950Thr missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0