TB-Profiler result

Run: SRR18002950
Summary

Run ID: SRR18002950

Sample name:

Date: 03-04-2023 19:11:00

Number of reads: 1043706

Percentage reads mapped: 39.92

Strain: lineage2.2.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.99
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 0.87 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 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 7873 p.Pro191Leu missense_variant 0.12
gyrA 8187 c.886C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575492 c.145C>T synonymous_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620325 c.435G>A synonymous_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759698 c.-109C>T upstream_gene_variant 0.2
rpoB 761331 p.Pro509Ser missense_variant 0.14
rpoB 761713 p.Val636Asp missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.92
rpoC 764605 c.1236G>C synonymous_variant 0.18
rpoC 764611 c.1242G>C synonymous_variant 0.18
rpoC 764632 c.1263T>C synonymous_variant 0.18
rpoC 764641 c.1272C>T synonymous_variant 0.19
rpoC 764650 c.1281G>T synonymous_variant 0.17
rpoC 764656 c.1287C>G synonymous_variant 0.1
rpoC 764663 p.Val432Thr missense_variant 0.15
rpoC 764668 c.1299C>T synonymous_variant 0.15
rpoC 764672 p.Gln435Glu missense_variant 0.15
rpoC 764695 c.1326T>C synonymous_variant 0.15
rpoC 764705 p.Leu446Lys missense_variant 0.14
rpoC 764716 c.1347G>C synonymous_variant 0.14
rpoC 764858 p.Leu497Met missense_variant 0.12
rpoC 764872 c.1503A>G synonymous_variant 0.12
rpoC 764875 c.1506C>G synonymous_variant 0.11
rpoC 764887 c.1518G>C synonymous_variant 0.11
rpoC 764888 c.1519T>C synonymous_variant 0.11
rpoC 764893 c.1524T>C synonymous_variant 0.1
rpoC 764902 c.1533C>G synonymous_variant 0.1
rpoC 766257 p.Arg963His missense_variant 0.2
rpoC 766721 p.Pro1118Thr missense_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776452 p.Gly677Ser missense_variant 0.18
mmpL5 778323 p.Leu53Pro missense_variant 0.11
mmpR5 779240 p.Ala84Val missense_variant 0.15
mmpR5 779423 p.Tyr145Cys missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801361 p.Val185Phe missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.4
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.4
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.4
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.4
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.33
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.67
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.5
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.5
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.75
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.6
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.4
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.4
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.4
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.33
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.29
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.27
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.27
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.18
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.18
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.25
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.22
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.22
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.22
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.33
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.22
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.22
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.22
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.22
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.22
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.4
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.5
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.5
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.67
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.5
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.5
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.4
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.75
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.67
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.67
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.67
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.67
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.67
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.75
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.75
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.75
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.8
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.87
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.71
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.88
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.85
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.87
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.22
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.6
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.77
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.89
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.14
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.91
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.9
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.83
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.16
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.16
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.18
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.86
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.86
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.18
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.77
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.89
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.73
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.88
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.7
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.62
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.71
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.62
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.55
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.55
rrl 1476524 n.2868delA non_coding_transcript_exon_variant 0.62
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.67
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.4
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.33
rrl 1476704 n.3053dupC non_coding_transcript_exon_variant 0.17
inhA 1674554 p.Lys118Arg missense_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834580 p.Lys347Glu missense_variant 0.13
tlyA 1917808 c.-132C>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918388 p.Leu150Arg missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155346 p.Ala256Thr missense_variant 0.93
katG 2156196 c.-85C>T upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170573 c.40T>C synonymous_variant 0.11
Rv1979c 2222993 p.Ala58Thr missense_variant 0.12
Rv1979c 2223030 c.135C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519080 c.966G>A synonymous_variant 0.12
eis 2714214 c.1119C>T synonymous_variant 0.18
folC 2746624 c.975C>T synonymous_variant 0.14
ribD 2986837 c.-2T>A upstream_gene_variant 0.25
ribD 2987035 p.Gly66Asp missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339062 c.-56G>A upstream_gene_variant 0.12
Rv3083 3449641 p.Asn380Asp missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
ddn 3986928 p.Tyr29His missense_variant 0.11
clpC1 4040021 c.684A>G synonymous_variant 0.1
panD 4044040 p.Pro81Leu missense_variant 0.15
panD 4044066 c.216C>T synonymous_variant 0.12
embC 4240137 p.Ala92Val missense_variant 0.13
embC 4240930 p.Trp356* stop_gained 0.14
embC 4241958 p.Arg699Gln missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.19
embB 4246555 c.42G>C synonymous_variant 0.21
embB 4246556 p.Ala15Pro missense_variant 0.21
embB 4246563 p.Leu17Trp missense_variant 0.26
embB 4246567 c.54G>T synonymous_variant 0.18
embB 4247055 p.Leu181Gln missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4270021 c.-188T>C upstream_gene_variant 0.11
whiB6 4338299 c.223C>T synonymous_variant 0.12
whiB6 4338575 c.-54A>G upstream_gene_variant 0.94
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 4408398 c.-196C>T upstream_gene_variant 0.13