TB-Profiler result

Run: ERR2229540
Summary

Run ID: ERR2229540

Sample name:

Date: 31-03-2023 17:18:08

Number of reads: 1059521

Percentage reads mapped: 97.99

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.16 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
fgd1 491533 p.Pro251Thr missense_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.38
ccsA 620145 p.Tyr85* stop_gained 0.15
rpoC 764161 c.792G>A synonymous_variant 0.15
rpoC 764326 c.957G>C synonymous_variant 0.18
rpoC 764338 p.Glu323Asp missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304371 p.His481Asp missense_variant 0.17
Rv1258c 1406436 p.Ser302* stop_gained 0.4
Rv1258c 1406449 c.892C>T synonymous_variant 0.2
Rv1258c 1406492 c.849C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.14
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.26
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.16
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.19
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.21
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.24
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.23
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.12
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.14
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.21
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.16
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.17
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.19
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.2
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.2
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.19
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.17
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.12
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.16
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.14
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.14
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.11
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.17
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.17
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.12
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.12
rrs 1473094 n.1249T>G non_coding_transcript_exon_variant 0.12
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.14
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 0.14
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.14
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.14
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.1
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.24
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.34
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.33
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.23
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.19
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.19
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.22
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.3
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.26
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.14
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.13
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 0.13
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.13
rrl 1474269 n.612C>A non_coding_transcript_exon_variant 0.12
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.12
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.12
rrl 1474467 n.810A>T non_coding_transcript_exon_variant 0.16
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.18
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.11
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.28
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.27
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.28
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.26
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.26
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.26
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.26
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.26
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.26
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.38
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.28
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.26
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.25
rrl 1475215 n.1558A>G non_coding_transcript_exon_variant 0.22
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.25
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.19
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.32
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.25
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.23
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.23
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.18
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.12
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.12
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.19
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.19
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.13
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.12
rrl 1475991 n.2334T>A non_coding_transcript_exon_variant 0.12
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.13
rrl 1475996 n.2339T>G non_coding_transcript_exon_variant 0.13
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.24
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.24
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.24
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.23
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.32
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.4
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.41
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.39
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.17
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.16
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.19
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.12
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.11
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.11
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.18
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.18
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.23
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.18
rrl 1476595 n.2938C>T non_coding_transcript_exon_variant 0.17
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.34
fabG1 1674176 p.Gly246Ala missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.13
PPE35 2167868 c.2745A>C synonymous_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.12
PPE35 2167967 c.2646A>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2169939 p.Gly225Ala missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.55
PPE35 2170147 p.Ser156Ala missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289911 c.-670G>T upstream_gene_variant 0.15
pncA 2290134 c.-893G>T upstream_gene_variant 0.25
kasA 2518093 c.-22C>A upstream_gene_variant 0.14
folC 2746538 p.His354Arg missense_variant 0.18
folC 2746971 p.Ala210Thr missense_variant 0.15
folC 2746972 c.627C>A synonymous_variant 0.15
pepQ 2860155 c.264C>A synonymous_variant 0.13
pepQ 2860489 c.-71G>A upstream_gene_variant 0.13
Rv2752c 3064842 c.1350C>T synonymous_variant 0.25
fbiD 3339594 p.His159Gln missense_variant 0.15
fbiD 3339734 p.Ala206Gly missense_variant 0.22
Rv3236c 3612571 c.546C>G synonymous_variant 0.15
Rv3236c 3613096 c.21G>A synonymous_variant 0.15
fbiB 3641660 p.Asp42Glu missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.3
clpC1 4039634 p.Glu357Gly missense_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.14
clpC1 4039782 p.Leu308Pro missense_variant 0.17
embA 4242631 c.-602G>A upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244914 p.Leu561Pro missense_variant 0.17
embA 4245780 p.Ala850Ser missense_variant 0.14
embA 4246295 p.Trp1021* stop_gained 0.14
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.4
aftB 4267671 p.Ala389Val missense_variant 0.13
aftB 4267817 c.1020G>C synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0