TB-Profiler result

Run: SRR5818630
Summary

Run ID: SRR5818630

Sample name:

Date: 04-04-2023 11:40:02

Number of reads: 647152

Percentage reads mapped: 88.98

Strain: lineage2.2.1

Drug-resistance: Other

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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 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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.17 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.2 kanamycin, capreomycin, aminoglycosides, amikacin
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 491722 p.Gly314* stop_gained 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
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 1417355 c.-8G>T upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.18
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.11
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.13
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.12
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.11
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.11
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.11
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.1
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.17
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.17
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.17
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.22
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.22
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.17
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.23
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.11
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.12
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.13
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.14
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.13
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.17
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.17
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.17
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.15
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.15
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.13
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.18
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.18
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.18
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.18
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.18
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.45
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.3
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.25
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.38
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>A non_coding_transcript_exon_variant 0.22
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.2
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.3
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.3
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.3
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.36
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.44
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.47
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.45
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.41
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.48
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.14
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.48
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.5
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.3
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.24
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.48
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.48
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.16
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.2
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
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
PPE35 2168876 p.Phe579Leu missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289514 c.-273C>A upstream_gene_variant 0.12
kasA 2519197 c.1083G>T synonymous_variant 0.19
eis 2714526 c.805_806delAC frameshift_variant 1.0
Rv2752c 3065711 p.Gly161Ser missense_variant 1.0
thyX 3067991 c.-46G>T upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474606 c.600A>G synonymous_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640744 p.Thr68Pro missense_variant 0.11
rpoA 3878536 c.-29G>T upstream_gene_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245272 c.2040G>T synonymous_variant 0.13
embB 4246584 p.Arg24Pro missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268548 p.Leu97Met missense_variant 0.22
ethR 4327709 p.Ala54Val missense_variant 0.12
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