TB-Profiler result

Run: ERR2660505
Summary

Run ID: ERR2660505

Sample name:

Date: 31-03-2023 22:52:55

Number of reads: 3135687

Percentage reads mapped: 69.36

Strain: lineage1.2.2.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.44 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 5075 c.-165C>T upstream_gene_variant 0.99
gyrB 6112 p.Met291Ile missense_variant 0.99
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 491060 p.Met93Thr missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620659 p.Arg257Cys missense_variant 0.99
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
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
rplC 800899 p.Ala31Thr missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.13
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.13
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.18
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.25
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.42
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.42
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.41
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.41
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.41
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.41
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.4
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.36
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.3
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.3
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.29
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.31
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.31
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.3
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.31
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.31
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.3
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.3
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.3
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.32
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.36
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.39
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.43
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.43
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.37
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.34
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.28
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.16
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.15
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.15
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.12
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.19
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.19
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.11
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.11
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.11
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.11
rrl 1475108 n.1451C>T non_coding_transcript_exon_variant 0.14
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.14
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.11
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.1
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.11
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.13
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.14
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.14
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.14
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.16
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.16
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.16
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.15
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.15
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.16
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.16
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.17
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.28
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.28
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.28
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.48
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.48
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.42
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.42
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.41
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.35
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.35
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.35
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.35
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.35
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.34
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.34
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.36
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.37
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.37
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.38
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.42
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.38
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.41
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.35
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.35
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.34
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.34
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.28
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.26
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.27
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.35
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
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
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
thyX 3068115 c.-170C>T upstream_gene_variant 1.0
thyA 3074034 c.438T>C 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
rpoA 3878578 c.-71C>A upstream_gene_variant 0.5
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_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
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4327450 c.-99G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0