TB-Profiler result

Run: SRR18002888
Summary

Run ID: SRR18002888

Sample name:

Date: 03-04-2023 19:08:24

Number of reads: 3530791

Percentage reads mapped: 85.42

Strain: lineage2.2.1

Drug-resistance: RR-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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
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 0.94 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.13 streptomycin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.23 streptomycin
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.99
mshA 576108 p.Ala254Gly missense_variant 0.31
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
embR 1416306 c.1041delC frameshift_variant 0.91
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.17
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.18
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.23
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.17
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.22
rrs 1472674 n.829T>C non_coding_transcript_exon_variant 0.15
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.22
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.23
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.19
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.29
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.14
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.14
rrl 1474476 n.819C>G non_coding_transcript_exon_variant 0.11
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.13
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.13
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.14
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.1
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.11
rrl 1475752 n.2095C>G non_coding_transcript_exon_variant 0.14
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.13
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.13
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.14
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.14
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.14
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.14
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.14
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.14
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.15
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.16
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.26
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.26
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.26
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.27
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.13
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.24
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.21
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.13
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T 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 0.13
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.14
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.14
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.16
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.19
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.18
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.24
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.19
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.19
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.28
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.28
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.25
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.26
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.26
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.16
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.39
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.22
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.24
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.11
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.16
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.12
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.16
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.16
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.17
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.17
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.1
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.11
rpsA 1833410 c.-132G>A upstream_gene_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
katG 2154959 p.Arg385Trp missense_variant 0.88
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168548 p.Thr689Ala missense_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726285 c.93C>T synonymous_variant 0.12
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
fbiB 3641812 p.Leu93Ser missense_variant 0.97
rpoA 3878567 c.-60C>G upstream_gene_variant 0.19
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 0.32
embB 4246548 p.Pro12Gln missense_variant 0.47
embB 4246555 c.42G>C synonymous_variant 0.49
embB 4246556 p.Ala15Pro missense_variant 0.48
embB 4246563 p.Leu17Trp missense_variant 0.47
embB 4246567 c.54G>T synonymous_variant 0.3
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