TB-Profiler result

Run: DRR213597
Summary

Run ID: DRR213597

Sample name:

Date: 31-03-2023 07:54:09

Number of reads: 2839393

Percentage reads mapped: 68.37

Strain: lineage2.2.2

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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 760314 p.Val170Phe missense_variant 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 0.99 isoniazid, 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 8396 c.1095C>T synonymous_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764387 c.1018T>C synonymous_variant 0.13
rpoC 764392 c.1023C>T synonymous_variant 0.14
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.12
rpoC 764410 c.1041G>C synonymous_variant 0.13
rpoC 764428 c.1059G>C synonymous_variant 0.12
rpoC 764434 c.1065A>G synonymous_variant 0.11
rpoC 764435 c.1066A>C synonymous_variant 0.11
rpoC 764446 p.Asp359Glu missense_variant 0.11
rpoC 764450 p.Gly361Arg missense_variant 0.11
rpoC 764455 c.1086G>C synonymous_variant 0.11
rpoC 764458 c.1089G>C synonymous_variant 0.11
rpoC 764461 p.Glu364Asp missense_variant 0.11
rpoC 764470 c.1101C>G synonymous_variant 0.12
rpoC 764471 p.Asn368Arg missense_variant 0.11
rpoC 764485 c.1116G>C synonymous_variant 0.16
rpoC 764497 c.1128A>G synonymous_variant 0.16
rpoC 764498 p.Ser377Ala missense_variant 0.15
rpoC 764521 c.1152T>C synonymous_variant 0.14
rpoC 764527 c.1158C>G synonymous_variant 0.12
rpoC 764587 c.1218C>G synonymous_variant 0.11
rpoC 764819 p.Trp484Ala missense_variant 0.28
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777661 c.819delC frameshift_variant 1.0
mmpS5 779615 c.-710C>G 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 1472887 n.1042G>C non_coding_transcript_exon_variant 0.18
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.48
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.48
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.47
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.47
rrs 1472970 n.1125C>T non_coding_transcript_exon_variant 0.46
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.47
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.47
rrs 1472975 n.1130T>G non_coding_transcript_exon_variant 0.46
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.46
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.45
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.45
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.45
rrs 1472993 n.1148G>A non_coding_transcript_exon_variant 0.45
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.44
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.44
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.44
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.44
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.39
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.33
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.13
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.38
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.38
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.38
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.55
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.61
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.6
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.6
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.61
rrl 1476417 n.2760T>C non_coding_transcript_exon_variant 0.62
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.64
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.65
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.6
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.58
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.43
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.31
rrl 1476516 n.2859G>A non_coding_transcript_exon_variant 0.28
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.28
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.28
rrl 1476521 n.2864C>T non_coding_transcript_exon_variant 0.28
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.28
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.28
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.28
rrl 1476532 n.2876_2877insCG non_coding_transcript_exon_variant 0.28
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.27
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.27
rrl 1476588 n.2931A>G non_coding_transcript_exon_variant 0.22
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.17
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 1.0
PPE35 2167928 c.2685G>T synonymous_variant 0.99
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 1.0
alr 3841156 p.Leu89Phe missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4407982 p.Leu74Ser missense_variant 1.0