TB-Profiler result

Run: SRR9971163
Summary

Run ID: SRR9971163

Sample name:

Date: 04-04-2023 23:14:09

Number of reads: 1787070

Percentage reads mapped: 37.86

Strain: lineage4.4.1.1.1

Drug-resistance: MDR-TB

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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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 Euro-American S;Orphans 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.59 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289142 p.Tyr34Asp missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
mshA 576108 p.Ala254Gly missense_variant 0.19
rpoB 762149 c.2343G>C synonymous_variant 0.1
rpoC 764575 c.1206T>G synonymous_variant 0.1
rpoC 764577 p.Ser403Cys missense_variant 0.1
rpoC 766487 p.Pro1040Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461048 p.Asp2Asn missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.5
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.5
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.5
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.5
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.4
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.4
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.5
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.57
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.6
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.38
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.38
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.38
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.38
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.29
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.25
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.25
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.29
rrs 1472301 n.456C>T non_coding_transcript_exon_variant 0.22
rrs 1472317 n.472G>T non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.2
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.22
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.33
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.33
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.4
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.6
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.67
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.75
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.67
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.4
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.62
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.82
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.45
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.45
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.5
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.5
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.45
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.45
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.45
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.54
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.58
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.59
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.59
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.4
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.55
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.4
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.4
rrs 1473265 n.1420C>T non_coding_transcript_exon_variant 0.15
rrl 1473664 n.7G>A non_coding_transcript_exon_variant 0.11
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.25
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.29
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.29
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.33
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.4
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.25
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.25
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.42
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.42
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.17
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.33
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.33
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.31
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.38
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.38
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.42
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.38
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.38
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.38
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.33
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.38
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.36
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.38
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.38
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.48
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.21
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.68
rrl 1476354 n.2697A>G non_coding_transcript_exon_variant 0.28
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.76
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.29
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.77
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.77
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.75
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.75
rrl 1476388 n.2731T>C non_coding_transcript_exon_variant 0.32
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.39
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.33
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.45
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.71
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.77
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.44
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.36
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.65
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064993 p.Trp400* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339287 p.Arg57Leu missense_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
Rv3083 3448482 c.-22G>T upstream_gene_variant 0.13
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.21
embB 4247028 p.Leu172Arg missense_variant 0.22
ubiA 4269308 p.Phe176Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0