TB-Profiler result

Run: SRR1013611
Summary

Run ID: SRR1013611

Sample name:

Date: 02-04-2023 15:59:08

Number of reads: 1493489

Percentage reads mapped: 27.31

Strain: lineage4

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
lineage4 Euro-American LAM;T;S;X;H None 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 2155693 p.Ser140Asn missense_variant 0.29 isoniazid
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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762881 p.Met1025Ile missense_variant 0.21
rpoC 762893 c.-477C>T upstream_gene_variant 0.33
rpoC 762896 c.-474G>C upstream_gene_variant 0.32
rpoC 762917 c.-453C>G upstream_gene_variant 0.48
rpoC 762920 c.-450C>T upstream_gene_variant 0.5
rpoC 762923 c.-447C>G upstream_gene_variant 0.48
rpoB 762925 p.Thr1040Ile missense_variant 0.47
rpoC 762929 c.-441G>T upstream_gene_variant 0.45
rpoB 762939 p.Met1045Leu missense_variant 0.43
rpoB 762942 p.Ile1046Val missense_variant 0.42
rpoC 762965 c.-405T>C upstream_gene_variant 0.28
rpoC 762980 c.-390T>C upstream_gene_variant 0.22
rpoC 762989 c.-381G>C upstream_gene_variant 0.18
rpoC 762995 c.-375G>C upstream_gene_variant 0.14
rpoC 764348 p.Met327Leu missense_variant 0.16
rpoC 764355 p.Gln329Pro missense_variant 0.15
rpoC 764398 c.1029G>C synonymous_variant 0.15
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.15
rpoC 764410 c.1041G>T synonymous_variant 0.15
rpoC 764428 c.1059G>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305446 p.Gly839Ala missense_variant 1.0
Rv1258c 1406414 c.927G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.2
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.27
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.26
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.25
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.25
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.18
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.18
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.16
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.12
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.11
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.11
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.12
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.13
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.13
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.13
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.12
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.12
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.12
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 1.0
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.12
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.12
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.26
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.26
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.26
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.25
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.21
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.13
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.13
rrs 1472861 n.1016G>C non_coding_transcript_exon_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.19
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.23
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.22
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.21
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.22
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.22
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.24
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.23
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.24
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.15
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.19
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.19
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.21
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.35
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.38
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.45
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.44
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.42
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.4
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.39
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.34
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.31
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.32
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155613 p.Phe167Leu missense_variant 0.13
katG 2155614 c.498T>C synonymous_variant 0.14
katG 2155617 p.Ile165Met missense_variant 0.14
katG 2155626 c.486G>C synonymous_variant 0.14
katG 2155637 p.Leu159Ile missense_variant 0.14
katG 2155641 p.Lys157Arg missense_variant 0.15
katG 2155650 c.462G>A synonymous_variant 0.13
katG 2155655 p.Lys153Gln missense_variant 0.14
katG 2155661 p.Val151Ile missense_variant 0.21
katG 2155668 c.444G>C synonymous_variant 0.23
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.27
katG 2155704 c.408C>T synonymous_variant 0.23
katG 2155716 c.396T>C synonymous_variant 0.27
katG 2155722 c.390G>C synonymous_variant 0.3
katG 2155728 c.384G>C synonymous_variant 0.38
katG 2155735 p.Met126Gln missense_variant 0.38
katG 2155737 c.375C>T synonymous_variant 0.38
katG 2155741 p.Gly124Ala missense_variant 0.38
katG 2155743 c.369G>T synonymous_variant 0.33
PPE35 2167892 c.2721G>A synonymous_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726744 c.552G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245567 p.Glu779Gln missense_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0