TB-Profiler result

Run: SRR13861586
Summary

Run ID: SRR13861586

Sample name:

Date: 03-04-2023 09:35:31

Number of reads: 761632

Percentage reads mapped: 15.25

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 0.79 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 9275 c.1974G>A synonymous_variant 0.15
gyrA 9278 c.1977G>C synonymous_variant 0.15
gyrA 9281 c.1980C>G synonymous_variant 0.14
gyrA 9284 c.1983T>C synonymous_variant 0.14
gyrA 9296 c.1995T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Glu missense_variant 0.15
gyrA 9311 c.2010C>T synonymous_variant 0.14
gyrA 9323 c.2022C>G synonymous_variant 0.14
gyrA 9490 p.Gly730Asp missense_variant 1.0
fgd1 491231 p.Phe150Tyr missense_variant 0.93
rpoB 762218 c.2412T>G synonymous_variant 0.14
rpoC 763780 c.411C>G synonymous_variant 0.13
rpoC 763783 c.414G>C synonymous_variant 0.17
rpoC 763801 c.432C>G synonymous_variant 0.16
rpoC 763807 c.438T>C synonymous_variant 0.16
rpoC 763819 c.450G>C synonymous_variant 0.15
rpoC 763831 c.462A>G synonymous_variant 0.16
rpoC 763835 p.Ala156Met missense_variant 0.17
rpoC 763858 c.489A>G synonymous_variant 0.21
rpoC 763872 p.Gly168Ala missense_variant 0.17
rpoC 763876 p.Glu169Asp missense_variant 0.15
rpoC 763879 c.510A>G synonymous_variant 0.15
rpoC 763888 c.519G>C synonymous_variant 0.16
rpoC 763891 c.522G>C synonymous_variant 0.12
rpoC 763945 c.576T>C synonymous_variant 0.13
rpoC 764872 c.1503A>G synonymous_variant 0.12
rpoC 764893 c.1524T>C synonymous_variant 0.14
rpoC 766128 p.Ala920Gly missense_variant 1.0
rpsL 781503 c.-57T>C upstream_gene_variant 1.0
fbiC 1303099 c.170dupA frameshift_variant 1.0
fbiC 1304043 c.1116delC frameshift_variant 1.0
Rv1258c 1406861 p.Ile160Met missense_variant 1.0
Rv1258c 1407463 c.-123G>C upstream_gene_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.19
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.26
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.26
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.53
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.68
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.52
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.71
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.71
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.73
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.72
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.72
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.71
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.72
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.72
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.71
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.72
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.72
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.73
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.7
rrs 1472230 n.385C>T non_coding_transcript_exon_variant 0.18
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.69
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.69
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.68
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.61
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.56
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.44
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.41
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.26
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.26
rrs 1472303 n.458G>A non_coding_transcript_exon_variant 0.91
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.22
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.48
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.78
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.78
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.79
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.77
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.77
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.78
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.78
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.78
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.78
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.78
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.78
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.79
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.79
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.8
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.83
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.85
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.84
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.82
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.8
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.8
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.79
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.8
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.79
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.79
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.79
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.79
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.78
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.57
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.42
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.42
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.42
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.43
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.46
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.46
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.5
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.44
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.42
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.43
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.46
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.47
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.44
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.44
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.44
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.42
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.43
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.44
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.41
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.14
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.13
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.14
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.14
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.23
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.2
rrl 1473945 n.288T>C non_coding_transcript_exon_variant 0.2
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.24
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.18
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.12
rrl 1474235 n.578G>T non_coding_transcript_exon_variant 1.0
rrl 1475139 n.1482C>T non_coding_transcript_exon_variant 1.0
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.14
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.12
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.13
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.81
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.84
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.88
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.87
rrl 1476263 n.2606C>T non_coding_transcript_exon_variant 0.17
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.87
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.88
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.87
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.88
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.88
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.88
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.87
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.88
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.88
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.88
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.87
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.88
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.87
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.88
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.94
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.96
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.96
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.97
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.97
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.96
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.72
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.96
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.96
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.96
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.96
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.96
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.96
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.89
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.85
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.83
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.83
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.82
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.82
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.82
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.82
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.82
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.82
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.82
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.82
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.79
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.78
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.78
rrl 1476576 n.2919C>G non_coding_transcript_exon_variant 0.21
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.75
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.24
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.15
kasA 2518209 p.Thr32Arg missense_variant 1.0
folC 2746788 p.Ala271Pro missense_variant 1.0
thyX 3067214 p.Ser244Arg missense_variant 0.96
fbiD 3339396 c.279C>T synonymous_variant 1.0
rpoA 3877656 c.852T>C synonymous_variant 0.13
rpoA 3877678 p.Ala277Arg missense_variant 0.13
rpoA 3877680 c.828G>C synonymous_variant 0.13
rpoA 3877686 c.822A>G synonymous_variant 0.13
rpoA 3877704 c.804G>T synonymous_variant 0.13
rpoA 3878048 p.Ala154Ser missense_variant 0.96
clpC1 4038359 c.2346A>G synonymous_variant 0.12
clpC1 4038419 c.2286T>C synonymous_variant 0.15
clpC1 4038434 c.2271G>C synonymous_variant 0.13
clpC1 4038498 p.Ser736Thr missense_variant 0.13
clpC1 4038812 c.1893T>C synonymous_variant 0.12
clpC1 4038908 c.1797C>G synonymous_variant 0.13
clpC1 4038914 c.1791G>C synonymous_variant 0.14
clpC1 4038923 c.1782A>G synonymous_variant 0.17
clpC1 4038932 c.1773G>C synonymous_variant 0.18
clpC1 4038956 c.1749T>C synonymous_variant 0.14
clpC1 4038965 c.1740T>C synonymous_variant 0.14
clpC1 4038971 c.1734T>C synonymous_variant 0.14
clpC1 4038974 c.1731T>C synonymous_variant 0.13
clpC1 4038989 c.1716T>C synonymous_variant 0.13
clpC1 4038997 c.1708T>C synonymous_variant 0.14
clpC1 4039022 c.1683A>G synonymous_variant 0.14
clpC1 4039085 c.1620A>G synonymous_variant 0.13
clpC1 4039517 c.1188C>G synonymous_variant 0.14
clpC1 4040354 c.351A>G synonymous_variant 0.13
clpC1 4040363 c.342A>C synonymous_variant 0.13
clpC1 4040369 c.336C>G synonymous_variant 0.14
clpC1 4040411 c.294T>C synonymous_variant 0.14
embC 4241050 c.1188T>G synonymous_variant 0.12
embC 4241104 c.1242G>A synonymous_variant 0.14
embC 4241107 c.1245G>C synonymous_variant 0.14
embB 4247887 c.1374C>T synonymous_variant 0.12
embB 4247914 c.1401G>C synonymous_variant 0.12
embB 4248133 c.1620C>G synonymous_variant 0.12
embB 4248142 c.1629T>C synonymous_variant 0.14
embB 4248206 p.Ser565Gly missense_variant 0.14
embB 4248368 p.Leu619Val missense_variant 0.95
ethA 4327082 p.Cys131Ser missense_variant 1.0
ethA 4327097 p.Leu126His missense_variant 1.0
gid 4407792 c.411G>C synonymous_variant 1.0