TB-Profiler result

Run: SRR13861720
Summary

Run ID: SRR13861720

Sample name:

Date: 03-04-2023 09:38:52

Number of reads: 242604

Percentage reads mapped: 4.05

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.96 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
gyrA 7018 c.-284G>T upstream_gene_variant 1.0
gyrA 7427 c.126G>C synonymous_variant 0.13
gyrA 7472 c.171T>C synonymous_variant 0.14
gyrA 7475 c.174A>C synonymous_variant 0.14
gyrA 7484 c.183T>C synonymous_variant 0.15
gyrA 7487 c.186C>G synonymous_variant 0.14
gyrA 7523 c.222C>G synonymous_variant 0.14
gyrA 7532 c.231T>C synonymous_variant 0.19
gyrA 7541 c.240C>G synonymous_variant 0.2
gyrA 7571 c.270G>C synonymous_variant 0.27
gyrA 7585 p.Ser95Thr missense_variant 0.23
gyrA 7595 c.294C>G synonymous_variant 0.21
gyrA 7607 c.306C>G synonymous_variant 0.23
gyrA 7626 c.325C>T synonymous_variant 0.23
gyrA 7631 c.330G>C synonymous_variant 0.2
gyrA 7637 c.336C>G synonymous_variant 0.21
gyrA 7649 c.348C>T synonymous_variant 0.2
gyrA 7652 c.351C>T synonymous_variant 0.2
gyrA 7658 c.357A>G synonymous_variant 0.2
gyrA 7664 c.363T>C synonymous_variant 0.14
gyrA 7670 c.369A>G synonymous_variant 0.15
gyrA 7676 c.375G>C synonymous_variant 0.15
mshA 576668 c.1322dupA frameshift_variant&stop_gained 1.0
rpoB 761579 c.1773G>C synonymous_variant 0.17
rpoB 761606 c.1800C>G synonymous_variant 0.17
rpoB 761612 c.1806G>C synonymous_variant 0.17
rpoB 761615 c.1809A>C synonymous_variant 0.17
rpoB 761636 c.1830G>T synonymous_variant 0.18
rpoB 761645 c.1839C>G synonymous_variant 0.18
rpoB 761648 c.1842T>C synonymous_variant 0.17
rpoB 761657 c.1851C>G synonymous_variant 0.18
rpoB 761675 c.1869G>C synonymous_variant 0.14
rpoB 761687 c.1881C>T synonymous_variant 0.15
rpoB 761690 c.1884G>C synonymous_variant 0.18
rpoB 761765 c.1959T>C synonymous_variant 0.18
rpoB 761772 p.His656Ala missense_variant 0.18
rpoB 761778 p.Asn658Asp missense_variant 0.17
rpoB 761791 p.Arg662His missense_variant 0.15
rpoB 761813 c.2007T>C synonymous_variant 0.17
rpoB 761815 p.Ala670Glu missense_variant 0.17
rpoB 761834 c.2028T>C synonymous_variant 0.22
rpoB 761847 p.Cys681Ser missense_variant 0.25
rpoB 761852 c.2046C>G synonymous_variant 0.25
rpoB 761864 c.2058G>C synonymous_variant 0.25
rpoB 761873 c.2067A>G synonymous_variant 0.25
rpoB 761885 c.2079T>C synonymous_variant 0.25
rpoB 761891 c.2085G>C synonymous_variant 0.25
rpoB 762317 c.2511A>G synonymous_variant 0.18
rpoB 762329 c.2523G>C synonymous_variant 0.25
rpoB 762338 c.2532T>C synonymous_variant 0.15
rpoB 762347 c.2541T>C synonymous_variant 0.14
rpoB 762362 p.Glu852Asp missense_variant 0.2
rpoB 762369 c.2563T>C synonymous_variant 0.18
rpoC 762374 c.-996G>C upstream_gene_variant 0.17
rpoC 762380 c.-990T>G upstream_gene_variant 0.15
rpoC 762395 c.-975G>C upstream_gene_variant 0.17
rpoC 762398 c.-972T>C upstream_gene_variant 0.17
rpoC 762401 c.-969G>C upstream_gene_variant 0.18
rpoC 762404 c.-966T>C upstream_gene_variant 0.18
rpoC 762410 c.-960T>C upstream_gene_variant 0.17
rpoC 762416 c.-954A>G upstream_gene_variant 0.18
rpoC 762443 c.-927G>C upstream_gene_variant 0.23
rpoC 765100 c.1731G>C synonymous_variant 1.0
rpoC 765700 c.2331T>C synonymous_variant 0.17
rpoC 765734 c.2365T>C synonymous_variant 0.15
rpoC 765739 c.2370G>C synonymous_variant 0.15
rpoC 765751 c.2382C>G synonymous_variant 0.12
rpoC 765753 p.Asp795Ala missense_variant 0.12
rpoC 765772 c.2403C>G synonymous_variant 0.13
rpoC 765784 c.2415C>G synonymous_variant 0.14
rpoC 765811 c.2442T>C synonymous_variant 0.15
rpoC 765886 c.2517C>G synonymous_variant 0.14
rpoC 766843 c.3474T>C synonymous_variant 0.2
mmpL5 776059 p.Val808Met missense_variant 0.83
fbiC 1304599 p.Ile557Phe missense_variant 1.0
embR 1417348 c.-1A>T upstream_gene_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.38
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.59
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.59
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.83
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.88
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.69
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.91
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.9
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.91
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.91
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.89
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.91
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.92
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.91
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.91
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.92
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.92
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.92
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.92
rrs 1472230 n.385C>T non_coding_transcript_exon_variant 0.35
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.91
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.91
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.92
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.9
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.86
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.85
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.82
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.64
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.64
rrs 1472277 n.432C>A non_coding_transcript_exon_variant 0.33
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.75
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.89
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.94
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.93
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.93
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.92
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.94
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.94
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.95
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.96
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.96
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.95
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.95
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.96
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.94
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.94
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.96
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.96
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.96
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.95
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.95
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.95
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.96
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.96
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.96
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.96
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.95
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.97
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.97
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.92
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.44
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.29
rrs 1473080 n.1235C>A non_coding_transcript_exon_variant 0.25
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.25
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.29
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.33
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.83
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.83
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.83
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.83
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.86
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.86
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.86
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.83
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.83
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.83
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.83
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.83
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.83
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.78
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.83
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.83
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.82
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.83
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.77
rrl 1473631 n.-27T>C upstream_gene_variant 1.0
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.22
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.61
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.94
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.95
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.96
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.97
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.97
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.97
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.97
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.97
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.94
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.96
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.97
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.97
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.97
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.96
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.97
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.97
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.97
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.97
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.99
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.99
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.99
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.99
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.99
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.99
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.78
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.99
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.98
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.98
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.98
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.99
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.99
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.97
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.96
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.95
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.94
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.94
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.94
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.94
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.93
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.93
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.93
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.93
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.93
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.92
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.93
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.93
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.92
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.59
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.41
inhA 1673748 c.-454A>G upstream_gene_variant 0.22
rpsA 1833855 p.Lys105Thr missense_variant 0.9
rpsA 1833874 c.333T>C synonymous_variant 0.17
PPE35 2170030 p.Met195Leu missense_variant 1.0
kasA 2518276 p.Trp54* stop_gained 1.0
kasA 2518352 p.Met80Val missense_variant 1.0
kasA 2519116 c.1002C>G synonymous_variant 0.13
kasA 2519137 c.1023T>C synonymous_variant 0.15
kasA 2519167 c.1053T>C synonymous_variant 0.17
kasA 2519173 c.1059C>G synonymous_variant 0.17
kasA 2519197 c.1083G>C synonymous_variant 0.15
eis 2714478 c.855C>A synonymous_variant 1.0
pepQ 2860170 c.248_249insA frameshift_variant 1.0
Rv2752c 3065335 p.Leu286Arg missense_variant 1.0
thyX 3067500 p.Lys149Arg missense_variant 0.33
thyX 3067515 p.Ser144Thr missense_variant 0.29
thyX 3067526 c.420C>G synonymous_variant 0.29
thyX 3067530 p.Ala139Ser missense_variant 0.29
thyX 3067545 p.Glu134Ala missense_variant 0.38
thyX 3067549 p.Thr133Ala missense_variant 0.38
thyX 3067556 p.His130Gln missense_variant 0.29
thyX 3067559 p.Arg129Gln missense_variant 0.29
thyX 3067565 p.Asp127Glu missense_variant 0.25
thyX 3067570 p.Ala126Pro missense_variant 0.22
thyX 3067571 c.375C>T synonymous_variant 0.22
thyX 3067577 p.Glu123Asp missense_variant 0.22
thyX 3067582 p.Met122Leu missense_variant 0.22
thyX 3067586 c.360C>G synonymous_variant 0.22
thyX 3067601 c.345G>C synonymous_variant 0.25
thyX 3067604 c.342G>C synonymous_variant 0.25
thyX 3067610 p.Lys112Asn missense_variant 0.22
thyX 3067613 c.333G>A synonymous_variant 0.3
thyX 3067619 c.327A>C synonymous_variant 0.3
thyX 3067640 c.306G>C synonymous_variant 0.27
thyX 3067643 c.303C>T synonymous_variant 0.27
thyX 3067652 c.294T>C synonymous_variant 0.2
thyX 3067661 c.285C>G synonymous_variant 0.25
thyX 3067682 c.264G>C synonymous_variant 0.27
thyX 3067685 c.261A>G synonymous_variant 0.27
thyX 3067688 c.258G>C synonymous_variant 0.27
thyX 3067694 c.252G>C synonymous_variant 0.27
thyX 3067718 c.228C>G synonymous_variant 0.3
thyX 3067721 c.225T>C synonymous_variant 0.3
thyX 3067724 c.222G>A synonymous_variant 0.3
thyX 3067727 c.219A>C synonymous_variant 0.3
thyX 3067739 c.207T>C synonymous_variant 0.25
thyX 3067742 c.204A>C synonymous_variant 0.25
thyX 3067761 p.Arg62Lys missense_variant 0.18
thyX 3067765 p.Leu61Ile missense_variant 0.2
thyX 3067781 c.165C>G synonymous_variant 0.2
thyX 3067787 c.159G>A synonymous_variant 0.2
thyX 3067793 c.153T>C synonymous_variant 0.22
thyX 3067799 c.147G>A synonymous_variant 0.22
thyX 3067802 c.144C>G synonymous_variant 0.22
fbiB 3641019 c.-516G>A upstream_gene_variant 1.0
fbiB 3641941 p.Leu136Gln missense_variant 1.0
rpoA 3878335 p.Gly58Asp missense_variant 0.33
ddn 3986771 c.-73A>C upstream_gene_variant 0.29
clpC1 4038878 c.1827A>G synonymous_variant 0.2
clpC1 4038908 c.1797C>G synonymous_variant 0.22
clpC1 4038914 c.1791G>C synonymous_variant 0.25
clpC1 4038923 c.1782A>G synonymous_variant 0.38
clpC1 4038932 c.1773G>C synonymous_variant 0.22
clpC1 4038953 c.1752A>G synonymous_variant 0.22
clpC1 4038956 c.1749T>C synonymous_variant 0.2
clpC1 4038965 c.1740T>C synonymous_variant 0.2
clpC1 4038997 c.1708T>C synonymous_variant 0.25
clpC1 4039022 c.1683A>G synonymous_variant 0.29
clpC1 4040380 c.325T>C synonymous_variant 0.33
embC 4241292 p.Leu477Gln missense_variant 1.0
embC 4242011 p.Leu717Val missense_variant 1.0
embB 4245764 c.-750G>C upstream_gene_variant 0.29
embA 4245771 p.Asn847Ser missense_variant 0.29
embB 4245807 c.-707_-705delTTAinsCTG upstream_gene_variant 0.33
embA 4245820 p.Ser863Thr missense_variant 0.29
embB 4245830 c.-684G>C upstream_gene_variant 0.29
embB 4245845 c.-669T>G upstream_gene_variant 0.29
embB 4245848 c.-666C>G upstream_gene_variant 0.29
embB 4245860 c.-654C>G upstream_gene_variant 0.29
embB 4248720 p.Gly736Ala missense_variant 1.0
embB 4249432 c.2919A>G synonymous_variant 0.18
embB 4249444 c.2931T>C synonymous_variant 0.22
embB 4249676 p.Arg1055Cys missense_variant 1.0
aftB 4267622 c.1215G>C synonymous_variant 0.29
aftB 4267927 p.Ala304Ser missense_variant 1.0
whiB6 4338314 p.Ala70Thr missense_variant 0.29