TB-Profiler result

Run: SRR21675848
Summary

Run ID: SRR21675848

Sample name:

Date: 04-04-2023 02:39:14

Number of reads: 1582844

Percentage reads mapped: 81.84

Strain: lineage1.1.3.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 Indo-Oceanic NA 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
gid 4408100 c.102delG frameshift_variant 1.0 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
gyrB 5117 c.-123G>A upstream_gene_variant 0.67
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 0.99
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
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.16
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.18
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.19
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.22
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.24
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.29
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.29
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.31
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.32
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.2
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.3
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.25
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.28
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.28
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.22
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.26
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.26
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.19
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.28
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.2
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.19
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.25
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.17
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.14
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.21
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.12
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.14
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.14
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.12
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.1
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.11
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.12
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.14
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.27
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.26
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.25
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.25
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.25
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.25
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.25
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.26
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.27
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.28
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.3
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.3
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.32
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.31
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.24
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.31
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.31
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.31
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.26
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.17
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.17
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.14
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.17
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.18
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.19
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.2
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.2
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.18
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.18
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.2
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.19
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.15
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.14
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.15
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.14
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 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289627 c.-386C>T upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
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 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.98
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