TB-Profiler result

Run: ERR5865993

Summary

Run ID: ERR5865993

Sample name:

Date: 02-04-2023 00:26:38

Number of reads: 2501221

Percentage reads mapped: 77.01

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4326705 c.768delG frameshift_variant 1.0 ethionamide, 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762286 p.Arg827Leu missense_variant 0.96
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764428 c.1059G>C synonymous_variant 0.11
rpoC 764434 c.1065A>G synonymous_variant 0.11
rpoC 764435 c.1066A>C synonymous_variant 0.11
rpoC 764441 p.Ile358Leu missense_variant 0.1
rpoC 764449 c.1080G>C synonymous_variant 0.1
rpoC 764452 c.1083T>C synonymous_variant 0.1
rpoC 764461 p.Glu364Asp missense_variant 0.11
rpoC 764471 p.Asn368Gln missense_variant 0.1
rpoC 764521 c.1152T>C synonymous_variant 0.12
rpoC 764536 c.1167G>T synonymous_variant 0.11
rpoC 764539 c.1170C>G synonymous_variant 0.11
rpoC 764548 c.1179G>A synonymous_variant 0.16
rpoC 764560 c.1191T>C synonymous_variant 0.21
rpoC 764575 c.1206T>C synonymous_variant 0.18
rpoC 764576 c.1207_1208delTCinsAG synonymous_variant 0.19
rpoC 764579 p.Asp404His missense_variant 0.19
rpoC 764582 p.Leu405Met missense_variant 0.18
rpoC 764605 c.1236G>T synonymous_variant 0.17
rpoC 764614 c.1245G>A synonymous_variant 0.15
rpoC 764623 c.1254C>T synonymous_variant 0.11
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.16
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.19
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.23
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.22
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.22
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.24
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.15
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.24
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.23
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.22
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.22
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.23
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.26
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.23
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.13
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.28
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.28
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.25
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.25
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.25
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.25
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.22
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.21
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.21
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.15
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.12
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.12
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.15
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.22
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.26
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.27
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.27
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.31
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.33
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.27
rrl 1474869 n.1212G>C non_coding_transcript_exon_variant 0.27
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.26
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.19
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.19
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.18
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.12
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.1
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.1
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.1
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.1
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.26
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.31
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.35
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.37
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.37
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.4
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.44
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.39
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.42
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.21
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.12
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.17
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.16
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.16
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.12
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.1
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.11
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 2170066 p.Ala183Thr missense_variant 0.12
ald 3086695 c.-125C>T 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
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 1.0
whiB6 4338563 c.-42G>T upstream_gene_variant 1.0
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
Rv1979c 2220764 c.-283_*954del transcript_ablation 1.0