TB-Profiler result

Run: SRR3675251
Summary

Run ID: SRR3675251

Sample name:

Date: 04-04-2023 05:24:10

Number of reads: 468642

Percentage reads mapped: 50.09

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 1.0 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.75 kanamycin, capreomycin, aminoglycosides, amikacin
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.15
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
fbiC 1302785 c.-146A>G upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.88
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.89
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.89
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.92
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.92
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.92
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.92
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.92
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.92
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.93
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.93
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.94
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.95
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.94
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.92
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.92
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.89
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.89
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.89
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.89
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.89
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.89
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.89
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.89
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.89
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.89
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.67
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.5
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.67
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.67
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.67
rrs 1473215 n.1370A>G non_coding_transcript_exon_variant 0.67
rrs 1473259 n.1414C>G non_coding_transcript_exon_variant 0.75
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.75
rrs 1473264 n.1419A>G non_coding_transcript_exon_variant 0.75
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.75
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.67
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.67
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.67
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.67
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.67
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.67
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.67
rrl 1475900 n.2243A>C non_coding_transcript_exon_variant 0.67
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.67
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.67
rrl 1475933 n.2276C>T non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.67
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 0.7
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.64
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.64
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.64
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.64
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.64
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.64
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.64
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.64
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.64
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.64
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.64
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.67
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.73
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.73
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.75
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.71
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.75
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.78
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.77
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.74
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.71
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.71
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.8
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.81
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.81
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.73
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.71
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170586 c.27G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073681 c.791G>A splice_region_variant&stop_retained_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642387 p.Thr285Ala missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038626 p.Met693Ile missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248542 p.Ala677Thr missense_variant 0.12
whiB6 4338504 c.18G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0