TB-Profiler result

Run: SRR12199474
Summary

Run ID: SRR12199474

Sample name:

Date: 03-04-2023 06:42:33

Number of reads: 225746

Percentage reads mapped: 98.07

Strain: lineage1.1

Drug-resistance: Sensitive

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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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 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
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
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760310 c.504G>T synonymous_variant 0.17
rpoB 760354 p.Glu183Gly missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 765958 c.2589C>A synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777908 c.573G>T synonymous_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801051 c.243G>A synonymous_variant 1.0
rplC 801215 p.Gly136Ala missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461126 p.Asp28Tyr missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.25
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.95
rrs 1472954 n.1109T>A non_coding_transcript_exon_variant 0.13
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.2
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 0.13
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.13
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.15
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.15
rrl 1475623 n.1966C>G non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.18
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.18
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.18
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.17
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.17
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.17
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.17
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.17
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.17
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.13
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.13
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.13
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.13
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.13
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.17
rpsA 1834407 p.Arg289His missense_variant 0.29
tlyA 1917906 c.-34G>T upstream_gene_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101676 p.Ala456Glu missense_variant 0.22
ndh 2102935 c.108C>T synonymous_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167814 c.2799C>T synonymous_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746171 c.1428G>T synonymous_variant 1.0
folC 2746588 c.1011C>A synonymous_variant 0.4
folC 2747264 p.Gly112Asp missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3841253 c.168C>T synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243709 c.477C>T synonymous_variant 0.33
embA 4243848 p.Val206Met missense_variant 1.0
embA 4246206 p.Pro992Thr missense_variant 0.29
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0