TB-Profiler result

Run: SRR11972227
Summary

Run ID: SRR11972227

Sample name:

Date: 03-04-2023 05:33:48

Number of reads: 1933114

Percentage reads mapped: 99.18

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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
rpoC 763031 c.-339T>C upstream_gene_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 1472598 n.753A>C non_coding_transcript_exon_variant 0.1
rrs 1472607 n.762G>T non_coding_transcript_exon_variant 0.12
rrs 1472608 n.763T>A non_coding_transcript_exon_variant 0.12
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.14
rrs 1472643 n.798A>T non_coding_transcript_exon_variant 0.14
rrs 1472644 n.799C>A non_coding_transcript_exon_variant 0.15
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.15
rrs 1472676 n.831_832insGA non_coding_transcript_exon_variant 0.15
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.15
rrs 1472680 n.836_842delCTTGGGA non_coding_transcript_exon_variant 0.15
rrs 1472690 n.846dupG non_coding_transcript_exon_variant 0.14
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.14
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.21
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.17
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.12
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.14
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.12
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.13
rrs 1473006 n.1161A>G non_coding_transcript_exon_variant 0.12
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.14
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.13
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.14
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.12
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.12
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.12
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.13
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
rrl 1476288 n.2635_2643delGCACCCCCG non_coding_transcript_exon_variant 0.13
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.12
rrl 1476301 n.2644_2645insCGGTGGCTT non_coding_transcript_exon_variant 0.12
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.11
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.11
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.1
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.37
PPE35 2170053 p.Thr187Ser missense_variant 0.36
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
rpoA 3877960 p.Val183Gly missense_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244816 c.1584G>A synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_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