TB-Profiler result

Run: SRR13861224
Summary

Run ID: SRR13861224

Sample name:

Date: 03-04-2023 09:26:34

Number of reads: 1633948

Percentage reads mapped: 27.26

Strain: lineage4.9

Drug-resistance: Sensitive

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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
lineage4.9 Euro-American (H37Rv-like) T1 None 0.98
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
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 6624 p.Ser462* stop_gained 0.97
gyrA 7285 c.-17T>C upstream_gene_variant 1.0
gyrA 7637 c.336C>G synonymous_variant 0.16
gyrA 7649 c.348C>T synonymous_variant 0.14
gyrA 7697 c.396C>G synonymous_variant 0.15
gyrA 7715 c.414G>C synonymous_variant 0.14
gyrA 7728 c.427_429delAGGinsCGC synonymous_variant 0.16
gyrA 7760 c.459C>T synonymous_variant 0.17
gyrA 7763 c.462T>C synonymous_variant 0.16
gyrA 7799 c.498A>G synonymous_variant 0.17
gyrA 7835 c.534A>G synonymous_variant 0.21
gyrA 7838 c.537C>G synonymous_variant 0.21
gyrA 7859 c.558A>C synonymous_variant 0.19
gyrA 7862 c.561C>G synonymous_variant 0.19
gyrA 7865 c.564T>C synonymous_variant 0.19
gyrA 8798 c.1497C>T synonymous_variant 1.0
rpoB 761165 c.1359G>C synonymous_variant 0.15
rpoB 761222 c.1416G>C synonymous_variant 0.15
rpoB 762218 c.2412T>G synonymous_variant 0.16
rpoB 762254 c.2448T>C synonymous_variant 0.19
rpoB 762266 c.2460T>C synonymous_variant 0.17
rpoB 762284 c.2478G>C synonymous_variant 0.17
rpoB 762293 c.2487T>C synonymous_variant 0.18
rpoB 762317 c.2511A>G synonymous_variant 0.2
rpoB 762329 c.2523G>C synonymous_variant 0.2
rpoB 762338 c.2532T>C synonymous_variant 0.2
rpoB 762347 c.2541T>C synonymous_variant 0.19
rpoB 762362 p.Glu852Asp missense_variant 0.18
rpoB 762369 c.2563T>C synonymous_variant 0.18
rpoC 762374 c.-996G>C upstream_gene_variant 0.16
rpoC 762380 c.-990T>G upstream_gene_variant 0.17
rpoC 762395 c.-975G>C upstream_gene_variant 0.16
rpoC 762398 c.-972T>C upstream_gene_variant 0.15
rpoC 762404 c.-966T>C upstream_gene_variant 0.15
rpoC 762410 c.-960T>C upstream_gene_variant 0.17
rpoC 762416 c.-954A>G upstream_gene_variant 0.16
rpoC 762443 c.-927G>C upstream_gene_variant 0.15
rpoC 762989 c.-381G>C upstream_gene_variant 0.2
rpoC 762995 c.-375G>T upstream_gene_variant 0.2
rpoC 763444 c.75T>C synonymous_variant 0.14
rpoC 763456 c.87A>G synonymous_variant 0.16
rpoC 763468 c.99G>C synonymous_variant 0.16
rpoC 763486 c.117T>C synonymous_variant 0.19
rpoC 763528 c.159G>A synonymous_variant 0.19
rpoC 763546 c.177A>G synonymous_variant 0.2
rpoC 763570 c.201G>C synonymous_variant 0.22
rpoC 763594 c.225C>T synonymous_variant 0.17
rpoC 763633 c.264T>C synonymous_variant 0.2
rpoC 763636 c.267T>C synonymous_variant 0.18
rpoC 763642 c.273G>C synonymous_variant 0.19
rpoC 763658 c.289_291delCTTinsTTG synonymous_variant 0.19
rpoC 763675 c.306C>G synonymous_variant 0.19
rpoC 763696 c.327T>C synonymous_variant 0.17
rpoC 763702 c.333C>G synonymous_variant 0.17
rpoC 763708 c.339G>A synonymous_variant 0.15
rpoC 763714 c.345G>C synonymous_variant 0.15
rpoC 763717 c.348T>C synonymous_variant 0.16
rpoC 763723 c.354G>C synonymous_variant 0.17
rpoC 763732 c.363C>G synonymous_variant 0.18
rpoC 763735 c.366G>C synonymous_variant 0.19
rpoC 763744 c.375G>C synonymous_variant 0.19
rpoC 763765 c.396T>C synonymous_variant 0.14
rpoC 763768 c.399C>G synonymous_variant 0.14
rpoC 763780 c.411C>G synonymous_variant 0.15
rpoC 763783 c.414G>C synonymous_variant 0.15
rpoC 764438 c.1069_1070insA frameshift_variant 0.89
rpoC 765478 c.2109T>C synonymous_variant 0.14
rpoC 765499 c.2130C>G synonymous_variant 0.17
rpoC 765508 c.2139C>G synonymous_variant 0.16
rpoC 765553 c.2184C>T synonymous_variant 0.17
rpoC 765556 c.2187G>C synonymous_variant 0.16
rpoC 765559 c.2190G>C synonymous_variant 0.16
rpoC 765578 c.2209C>T synonymous_variant 0.14
rpoC 765583 c.2214G>T synonymous_variant 0.14
rpoC 765613 p.His748Gln missense_variant 0.15
rpoC 765628 c.2259G>C synonymous_variant 0.14
rpoC 766345 c.2976T>C synonymous_variant 0.13
rpoC 766348 c.2979A>G synonymous_variant 0.13
rpoC 766384 c.3015A>G synonymous_variant 0.18
rpoC 766390 c.3021C>T synonymous_variant 0.18
rpoC 766408 c.3039C>T synonymous_variant 0.17
rpoC 766426 c.3057C>T synonymous_variant 0.17
rpoC 766447 c.3078T>C synonymous_variant 0.15
rpoC 766522 c.3153C>G synonymous_variant 0.18
rpoC 766528 c.3159T>C synonymous_variant 0.13
rpoC 766531 c.3162G>T synonymous_variant 0.13
rpoC 766861 c.3492G>C synonymous_variant 0.14
mmpL5 775795 p.Ala896Ser missense_variant 1.0
rpsL 781715 c.156T>C synonymous_variant 0.14
rpsL 781728 c.169T>C synonymous_variant 0.15
rpsL 781736 c.177T>C synonymous_variant 0.14
rpsL 781754 c.195G>C synonymous_variant 0.15
rpsL 781760 c.201T>C synonymous_variant 0.18
rpsL 781793 c.234G>C synonymous_variant 0.18
rpsL 781832 c.273T>C synonymous_variant 0.17
rpsL 781841 c.282C>G synonymous_variant 0.18
rpsL 781859 c.300T>C synonymous_variant 0.16
rpsL 781892 c.333A>G synonymous_variant 0.16
rpsL 781898 c.339A>T synonymous_variant 0.17
rpsL 781916 c.357T>C synonymous_variant 0.13
rplC 800874 c.66A>G synonymous_variant 0.14
rplC 800889 c.81C>G synonymous_variant 0.15
fbiC 1303593 c.663G>A synonymous_variant 0.93
embR 1416428 c.919_920insT frameshift_variant 1.0
rrs 1471798 n.-48G>A upstream_gene_variant 1.0
rrs 1472913 n.1068G>C non_coding_transcript_exon_variant 0.81
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.16
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.15
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.14
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.12
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.16
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.13
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.15
rrl 1475015 n.1358C>T non_coding_transcript_exon_variant 0.12
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.13
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.14
rrl 1476167 n.2510T>A non_coding_transcript_exon_variant 0.91
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.5
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.57
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.56
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.56
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.56
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.6
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.59
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.61
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.61
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.6
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.59
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.6
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.62
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.61
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.6
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.6
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.57
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.57
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.53
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.53
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.12
inhA 1674226 p.Arg9Trp missense_variant 1.0
rpsA 1833352 c.-190C>A upstream_gene_variant 1.0
rpsA 1833710 p.Tyr57Asp missense_variant 0.91
rpsA 1834666 c.1125G>C synonymous_variant 0.14
rpsA 1834669 c.1128G>C synonymous_variant 0.14
rpsA 1834711 c.1170C>T synonymous_variant 0.88
ndh 2102326 c.717G>T synonymous_variant 1.0
Rv1979c 2222739 c.426C>A synonymous_variant 1.0
Rv1979c 2222936 p.Ala77Thr missense_variant 1.0
kasA 2518621 c.507G>A synonymous_variant 0.13
kasA 2518663 c.549T>C synonymous_variant 0.16
kasA 2518672 c.558G>C synonymous_variant 0.15
kasA 2518687 c.573C>T synonymous_variant 0.14
kasA 2518702 c.588C>T synonymous_variant 0.13
kasA 2518732 c.618C>G synonymous_variant 0.15
kasA 2518741 c.627G>C synonymous_variant 0.16
kasA 2518747 c.633C>G synonymous_variant 0.16
kasA 2518783 c.669T>C synonymous_variant 0.15
eis 2714217 c.1115dupC frameshift_variant 1.0
eis 2714361 c.972C>A synonymous_variant 1.0
pepQ 2859813 p.Ile202Met missense_variant 0.98
pepQ 2860286 p.Val45Leu missense_variant 1.0
ribD 2987503 p.Gly222Val missense_variant 1.0
ald 3087394 p.Ala192Val missense_variant 1.0
ald 3087464 c.645C>T synonymous_variant 1.0
ald 3087512 c.693T>A synonymous_variant 1.0
clpC1 4038271 p.Pro812Ala missense_variant 0.14
clpC1 4038274 p.Gly811Ser missense_variant 0.13
clpC1 4038278 c.2427T>C synonymous_variant 0.15
clpC1 4038293 c.2412G>C synonymous_variant 0.17
clpC1 4038302 c.2403C>G synonymous_variant 0.16
clpC1 4038308 p.Val799Ile missense_variant 0.15
clpC1 4038317 c.2388G>C synonymous_variant 0.15
clpC1 4038347 c.2358G>C synonymous_variant 0.17
clpC1 4038356 c.2349T>C synonymous_variant 0.15
clpC1 4038368 c.2337T>C synonymous_variant 0.15
clpC1 4038388 c.2317T>C synonymous_variant 0.15
clpC1 4038398 c.2307G>T synonymous_variant 0.13
clpC1 4038956 c.1749T>C synonymous_variant 0.14
clpC1 4040522 c.183T>C synonymous_variant 0.14
embC 4241874 p.Leu671Arg missense_variant 1.0
embC 4242816 p.Trp985* stop_gained 0.98
embB 4248365 p.Val618Met missense_variant 0.96
aftB 4267893 p.Ile315Ser missense_variant 0.98
aftB 4268516 c.321A>G synonymous_variant 1.0
ethR 4326691 c.-858C>A upstream_gene_variant 1.0