TB-Profiler result

Run: SRR2101492
Summary

Run ID: SRR2101492

Sample name:

Date: 03-04-2023 23:44:59

Number of reads: 371524

Percentage reads mapped: 98.15

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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 0.3 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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
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 491096 p.Val105Ala missense_variant 0.15
mshA 575700 p.Glu118Gly missense_variant 0.12
ccsA 619831 c.-60T>G upstream_gene_variant 0.29
ccsA 620044 p.Gly52Arg missense_variant 0.17
rpoB 760473 p.Lys223Glu missense_variant 0.12
rpoB 761327 c.1521A>G synonymous_variant 0.18
rpoB 762218 c.2415_2416delGA frameshift_variant 0.13
rpoC 762764 c.-606G>A upstream_gene_variant 0.12
rpoC 764149 c.780G>A synonymous_variant 0.15
rpoC 764699 p.Pro444Ser missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765631 c.2262C>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776308 p.Asp725Asn missense_variant 0.11
mmpL5 776646 p.Val612Ala missense_variant 0.13
mmpS5 779637 c.-732T>C upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800725 c.-84C>T upstream_gene_variant 0.17
fbiC 1303905 c.975G>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471902 n.58delA non_coding_transcript_exon_variant 0.13
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.11
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.11
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.11
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.11
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.21
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.2
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.21
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.22
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.25
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.23
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.23
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.24
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.24
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.24
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.25
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.27
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.29
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.3
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.24
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.22
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.22
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.21
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.23
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.22
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.23
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.27
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.27
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.27
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.23
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.17
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.11
rrl 1473804 n.147T>C non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.16
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.21
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.44
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.44
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.44
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.42
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.42
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.44
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.44
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.42
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.42
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.44
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.44
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.44
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.42
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.42
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.44
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.5
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.5
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.48
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.44
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.46
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.48
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.57
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.52
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.52
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.52
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.43
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.33
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.28
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.28
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.28
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.28
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.28
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.26
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.26
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.26
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.26
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.23
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.2
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.19
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.18
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
rrl 1476793 n.3136A>G splice_region_variant&non_coding_transcript_exon_variant 0.29
inhA 1674288 c.89_101delAGGAGCAGGGCGC frameshift_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918244 p.Asp102Gly missense_variant 0.25
katG 2155759 p.Gly118Val missense_variant 0.14
PPE35 2167661 p.Ser984Arg missense_variant 0.11
PPE35 2168328 p.Pro762Gln missense_variant 0.12
PPE35 2168987 c.1626A>G synonymous_variant 0.11
Rv1979c 2222231 p.Met312Val missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288756 c.486T>C synonymous_variant 0.12
pncA 2289976 c.-735G>C upstream_gene_variant 0.18
pncA 2290107 c.-866T>A upstream_gene_variant 1.0
kasA 2518684 c.570C>A synonymous_variant 0.13
kasA 2519177 p.Ser355Pro missense_variant 0.17
eis 2715041 p.Arg98Ser missense_variant 0.17
ahpC 2726338 p.Val49Gly missense_variant 0.24
folC 2746821 p.Asp260Tyr missense_variant 0.22
pepQ 2859494 p.Gly309Trp missense_variant 0.25
pepQ 2860336 p.Ile28Thr missense_variant 0.1
pepQ 2860542 c.-124T>A upstream_gene_variant 0.11
Rv2752c 3065237 p.Ser319Pro missense_variant 0.11
Rv2752c 3066089 p.Glu35Lys missense_variant 0.12
thyX 3068160 c.-215T>C upstream_gene_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086820 c.1A>G start_lost 0.2
Rv3083 3449038 p.Lys179Glu missense_variant 0.17
Rv3083 3449361 c.858C>T synonymous_variant 0.14
Rv3083 3449843 p.Gly447Asp missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568583 p.Pro33Thr missense_variant 0.15
Rv3236c 3612366 p.Leu251Val missense_variant 0.22
fbiB 3641421 c.-114C>T upstream_gene_variant 0.14
fbiB 3642340 p.Asp269Gly missense_variant 0.29
clpC1 4038191 c.2514C>T synonymous_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038863 c.1842G>T synonymous_variant 0.29
embC 4241674 c.1812C>T synonymous_variant 0.29
embC 4242010 c.2148G>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245470 c.2238T>C synonymous_variant 0.2
embB 4248078 p.Asn522Ser missense_variant 0.17
embB 4249669 p.Tyr1052* stop_gained 0.2
aftB 4267494 p.Gly448Val missense_variant 0.12
ethA 4327402 p.Gln24His missense_variant 0.12
ethR 4327652 p.Asn35Ser missense_variant 0.14
ethR 4327688 p.Val47Asp missense_variant 0.17
ethA 4328215 c.-742C>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0