TB-Profiler result

Run: SRR8217919
Summary

Run ID: SRR8217919

Sample name:

Date: 04-04-2023 20:39:57

Number of reads: 3211823

Percentage reads mapped: 86.64

Strain: lineage2.2.1

Drug-resistance: HR-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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288919 p.Gly108Glu missense_variant 1.0 pyrazinamide
embB 4247622 p.Leu370Arg 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
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
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 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.21
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.23
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.22
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.21
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.21
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.23
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.22
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.22
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.22
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.22
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.22
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.24
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.26
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.26
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.24
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.24
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.15
rrs 1472954 n.1109T>G non_coding_transcript_exon_variant 0.25
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.25
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.25
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.25
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.25
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.24
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.24
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.24
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.25
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.25
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.24
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.25
rrs 1472992 n.1147A>C non_coding_transcript_exon_variant 0.24
rrs 1473002 n.1157G>C non_coding_transcript_exon_variant 0.22
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.25
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.25
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.27
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.21
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.15
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.13
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.13
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.14
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.12
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.12
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.13
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.17
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.18
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.16
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.16
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.16
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.16
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.16
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.16
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.16
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.16
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.16
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.16
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.17
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.27
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.35
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.37
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.38
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.3
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.3
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.3
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.3
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.29
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.3
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.29
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.32
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.32
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.33
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.41
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.47
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.49
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.48
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.47
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.48
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.45
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.43
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.43
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.44
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.41
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.36
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
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
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246553 c.40C>A synonymous_variant 0.3
embB 4246584 p.Arg24Pro missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338365 p.Cys53Arg 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