TB-Profiler result

Run: ERR2229554
Summary

Run ID: ERR2229554

Sample name:

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

Number of reads: 810726

Percentage reads mapped: 86.92

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 1472733 n.888G>A non_coding_transcript_exon_variant 0.26 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 6510 p.Arg424Leu missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491746 p.Glu322Gln missense_variant 0.22
mshA 576108 p.Ala254Gly missense_variant 0.22
mshA 576628 c.1281G>A synonymous_variant 0.18
rpoB 760898 c.1092C>T synonymous_variant 0.17
rpoB 761499 p.Val565Met missense_variant 0.14
rpoB 761509 p.Ser568Tyr missense_variant 0.12
rpoC 764609 p.Arg414Trp missense_variant 0.17
rpoC 764849 p.His494Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777084 p.Asn466Thr missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303261 p.Pro111Thr missense_variant 0.2
fbiC 1303560 c.630G>T synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304491 c.1561_1562insGT frameshift_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.16
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.23
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.21
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.21
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.21
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.22
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.23
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.19
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.2
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.25
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.18
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.18
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.18
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.18
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.24
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.2
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.19
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.18
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.19
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.23
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.28
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.28
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.21
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.22
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.18
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.16
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.16
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.19
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.21
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.23
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.23
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.28
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.3
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.21
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.21
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.21
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.15
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.21
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.23
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.33
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.2
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.15
rrl 1474236 n.579G>A non_coding_transcript_exon_variant 0.24
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.27
rrl 1474255 n.598C>T non_coding_transcript_exon_variant 0.19
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.12
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.15
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.15
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.15
rrl 1474903 n.1246T>A non_coding_transcript_exon_variant 0.15
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.15
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.17
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.13
rrl 1475163 n.1506T>G non_coding_transcript_exon_variant 0.15
rrl 1475507 n.1850C>T non_coding_transcript_exon_variant 0.18
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.24
rrl 1475552 n.1895G>C non_coding_transcript_exon_variant 0.29
rrl 1475574 n.1917C>A non_coding_transcript_exon_variant 0.11
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.21
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.22
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.18
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.19
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.12
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.13
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.24
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.16
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.13
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.12
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.12
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.14
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.14
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.14
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.14
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.14
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.14
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.16
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.18
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.21
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.5
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.64
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.68
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.48
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.49
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.57
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.57
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.47
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.34
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.37
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.37
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.29
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.26
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.14
rrl 1476640 n.2983C>A non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.32
fabG1 1673558 p.His40Pro missense_variant 0.2
fabG1 1674127 p.Ser230Gly missense_variant 0.2
inhA 1674162 c.-40C>A upstream_gene_variant 0.33
inhA 1674504 c.303C>G synonymous_variant 0.2
rpsA 1834676 p.Gly379Cys missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102146 c.897G>T synonymous_variant 0.29
ndh 2103097 c.-55C>T upstream_gene_variant 0.13
katG 2155117 p.Phe332Tyr missense_variant 0.14
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169287 c.1326T>C synonymous_variant 0.22
PPE35 2169581 c.1032C>G synonymous_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2222833 p.Ser111Tyr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289808 c.-567C>A upstream_gene_variant 0.18
kasA 2518606 c.492G>C synonymous_variant 0.33
kasA 2518609 p.Met165Ile missense_variant 0.33
kasA 2518864 c.750G>C synonymous_variant 0.14
kasA 2519140 c.1026G>C synonymous_variant 0.21
kasA 2519143 c.1029G>C synonymous_variant 0.21
folC 2746585 c.1014G>T synonymous_variant 0.14
folC 2747485 p.Trp38Cys missense_variant 0.22
ribD 2986892 p.Ser18Arg missense_variant 0.12
Rv2752c 3065757 c.435C>G synonymous_variant 0.15
thyA 3074190 c.282C>T synonymous_variant 0.14
ald 3087748 p.Thr310Asn missense_variant 0.22
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fprA 3474808 p.Val268Met missense_variant 0.5
fprA 3474977 p.Tyr324Cys missense_variant 0.33
fbiA 3640394 c.-149G>T upstream_gene_variant 0.17
fbiA 3641484 p.Asn314Lys missense_variant 0.2
fbiB 3642842 c.1308C>T synonymous_variant 0.18
alr 3840503 c.918T>C synonymous_variant 0.13
rpoA 3878344 p.Arg55Pro missense_variant 0.15
clpC1 4038782 c.1923G>C synonymous_variant 0.12
clpC1 4039018 p.Ser563Ala missense_variant 0.15
clpC1 4039022 c.1683A>G synonymous_variant 0.18
clpC1 4039031 c.1674T>C synonymous_variant 0.2
clpC1 4039654 p.Thr351Ser missense_variant 0.13
embC 4240655 p.Ala265Thr missense_variant 0.15
embC 4242558 p.Gln899Arg missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243896 p.Ala222Thr missense_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 1.0
embB 4247498 p.Pro329Thr missense_variant 0.18
embB 4247559 p.Trp349Leu missense_variant 0.13
aftB 4268389 c.447delG frameshift_variant 0.2
ethA 4326643 p.Asp277Glu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0