TB-Profiler result

Run: SRR3675361
Summary

Run ID: SRR3675361

Sample name:

Date: 04-04-2023 05:27:07

Number of reads: 1148038

Percentage reads mapped: 97.03

Strain: lineage1.1.2

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 0.99
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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
pncA 2289110 c.131delT frameshift_variant 0.1 pyrazinamide
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
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 6736 c.-566C>T upstream_gene_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
mshA 575278 c.-70C>A upstream_gene_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 767300 p.Gly1311Arg missense_variant 0.2
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
rpsL 781889 c.330C>T synonymous_variant 1.0
fbiC 1304574 c.1644C>T synonymous_variant 1.0
Rv1258c 1406503 p.Val280Leu missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.25
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.22
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.3
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.33
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.27
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.27
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.27
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.23
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.23
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.31
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.2
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.25
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.25
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.23
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.18
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 0.18
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.22
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.22
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.2
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.2
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.2
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.18
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.18
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.2
rrs 1473373 n.1528C>T non_coding_transcript_exon_variant 0.22
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.15
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.15
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.2
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.2
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.2
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.2
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.2
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.22
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.22
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.22
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.22
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.22
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.22
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.22
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.25
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.25
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.23
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.23
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.23
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.36
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.22
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.22
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.18
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.18
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.18
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.18
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.2
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.2
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.2
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.25
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.25
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.4
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.38
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.38
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.44
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153897 p.Val739Met missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.97
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
kasA 2518218 p.Gly35Asp missense_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 3448382 c.-122G>A upstream_gene_variant 0.12
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
clpC1 4040208 p.Ser166Phe missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240618 c.756C>T synonymous_variant 1.0
embC 4240655 p.Ala265Pro missense_variant 0.19
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.98
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 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338224 c.297delC frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338718 c.-197C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0