TB-Profiler result

Run: ERR9117696
Summary

Run ID: ERR9117696

Sample name:

Date: 02-04-2023 09:28:43

Number of reads: 850541

Percentage reads mapped: 37.66

Strain: lineage4.1.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 1472733 n.888G>A non_coding_transcript_exon_variant 0.29 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.37
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764023 c.654G>A synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777715 p.Ile256Val missense_variant 0.1
mmpR5 779371 p.Ala128Pro missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.67
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.75
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.75
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.75
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.75
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.5
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.75
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.75
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.75
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.75
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.75
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.75
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.75
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.4
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.4
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.4
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.4
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.33
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.29
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.29
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.25
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.25
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.18
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.22
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 1.0
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 1.0
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.67
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.33
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.5
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.67
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.5
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.5
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.5
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.5
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.5
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.5
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.5
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.5
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.5
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.5
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.5
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.5
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.5
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.64
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.45
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.64
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.73
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.67
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.6
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.6
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.55
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.55
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.5
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.4
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.5
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.46
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.46
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.46
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.47
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.53
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.47
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.47
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.38
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.44
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 1476425 n.2768G>T non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.25
PPE35 2170082 c.531T>G synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
thyX 3067582 p.Met122Val missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448594 p.Thr31Ser missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240057 c.195C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243600 p.Ala123Val missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0