TB-Profiler result

Run: SRR6045064
Summary

Run ID: SRR6045064

Sample name:

Date: 04-04-2023 11:52:12

Number of reads: 1327691

Percentage reads mapped: 70.83

Strain: lineage4.3.1.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.1 Euro-American (LAM) LAM9 None 0.99
lineage4.3.1.1 Euro-American (LAM) LAM9 None 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 0.97 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
gyrA 9683 c.2382G>A synonymous_variant 0.11
fgd1 491027 p.Asn82Thr missense_variant 0.28
fgd1 491380 p.Glu200* stop_gained 0.12
mshA 576751 p.Lys468Asn missense_variant 0.2
ccsA 620748 c.858T>G synonymous_variant 0.28
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407405 c.-65C>A upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471660 n.-186G>A upstream_gene_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.25
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.29
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.29
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.29
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.5
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.4
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.4
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.4
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.5
rrs 1472141 n.296G>A non_coding_transcript_exon_variant 0.15
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.15
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.62
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.46
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.46
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.83
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.97
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.97
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.95
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.94
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.51
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.97
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.97
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.97
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.97
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.96
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.96
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.96
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 1.0
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.27
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.71
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.96
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.96
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.97
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.97
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.86
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.8
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.8
rrs 1472806 n.961A>T non_coding_transcript_exon_variant 0.17
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.67
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.22
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.36
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.55
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.2
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.25
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.29
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.29
rrs 1473034 n.1189A>G non_coding_transcript_exon_variant 0.22
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.44
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.22
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.25
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.33
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.29
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.29
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.22
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.25
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.22
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.22
rrl 1473751 n.94C>T non_coding_transcript_exon_variant 0.25
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.4
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.44
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.33
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.22
rrl 1475713 n.2056C>T non_coding_transcript_exon_variant 1.0
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.5
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.5
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.67
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.71
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.71
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.71
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.71
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.67
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.67
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.5
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.67
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.67
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.5
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.5
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.5
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.5
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.67
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.67
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.67
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.67
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.67
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.67
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.71
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.75
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.78
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.81
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.86
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.85
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.91
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.76
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.77
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.77
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.15
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.87
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.5
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.4
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.43
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169090 p.Val508Glu missense_variant 0.11
PPE35 2169902 p.Leu237Phe missense_variant 0.11
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2169985 p.Ala210Thr missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518407 p.Ala98Val missense_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.32
thyX 3067966 c.-21G>A upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074654 c.-183T>G upstream_gene_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339688 p.Thr191Pro missense_variant 0.13
Rv3083 3449236 p.Arg245Gly missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethR 4327738 p.Tyr64His missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0