TB-Profiler result

Run: SRR11871413
Summary

Run ID: SRR11871413

Sample name:

Date: 03-04-2023 05:23:45

Number of reads: 5851166

Percentage reads mapped: 91.5

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 0.8 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Asn missense_variant 0.22 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761154 p.Ser450Met missense_variant 0.74 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.99 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289054 p.Asp63Ala missense_variant 0.37 pyrazinamide
pncA 2289073 p.His57Asp missense_variant 0.64 pyrazinamide
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
mshA 576108 p.Ala254Gly missense_variant 0.21
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762285 p.Arg827Cys missense_variant 0.24
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779181 c.198delG frameshift_variant 0.73
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 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472958 n.1114delT non_coding_transcript_exon_variant 0.12
rrs 1472975 n.1130T>G non_coding_transcript_exon_variant 0.11
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.13
rrs 1472986 n.1142delG non_coding_transcript_exon_variant 0.13
rrs 1472990 n.1146delG non_coding_transcript_exon_variant 0.13
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.14
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.12
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.13
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.12
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.13
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.13
rrs 1473094 n.1249T>C non_coding_transcript_exon_variant 0.12
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.14
rrs 1473109 n.1264T>C non_coding_transcript_exon_variant 0.13
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.13
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.13
rrs 1473115 n.1270G>C non_coding_transcript_exon_variant 0.12
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.11
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.12
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.11
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.11
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.11
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.12
rrl 1474830 n.1173A>C non_coding_transcript_exon_variant 0.1
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.11
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.15
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.17
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.15
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.14
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.15
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.16
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.16
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.16
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.18
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.18
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.27
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.28
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.31
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.31
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.31
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.27
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.27
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.24
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.2
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.16
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 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073715 p.Pro253Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448768 p.Ala89Thr missense_variant 0.74
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
embB 4246584 p.Arg24Pro missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.99
ethA 4326533 p.Thr314Ile 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 0.99