TB-Profiler result

Run: SRR13861573

Summary

Run ID: SRR13861573

Sample name:

Date: 03-04-2023 09:35:08

Number of reads: 154663

Percentage reads mapped: 15.48

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 0.99
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
gyrB 5709 p.Gly157Val missense_variant 1.0
gyrB 6169 c.930C>G synonymous_variant 0.33
gyrB 6190 c.951A>G synonymous_variant 0.33
gyrB 6209 c.970C>T synonymous_variant 0.33
gyrB 6214 c.975G>C synonymous_variant 0.43
gyrB 6217 c.978G>C synonymous_variant 0.43
gyrB 6223 c.984G>C synonymous_variant 0.43
gyrB 6242 p.Arg335Lys missense_variant 0.33
gyrB 6250 c.1011A>G synonymous_variant 0.4
gyrB 6253 c.1014G>C synonymous_variant 0.4
gyrB 6280 c.1041T>C synonymous_variant 0.4
gyrB 6286 c.1047T>C synonymous_variant 0.4
gyrB 6292 c.1053G>C synonymous_variant 0.4
gyrB 6295 c.1056A>G synonymous_variant 0.4
gyrB 6298 c.1059C>T synonymous_variant 0.33
gyrB 6299 c.1060C>T synonymous_variant 0.33
gyrA 6307 c.-995T>G upstream_gene_variant 0.33
gyrA 9028 p.Val576Ala missense_variant 1.0
gyrA 9335 c.2034G>C synonymous_variant 0.33
mshA 575587 c.240C>A synonymous_variant 0.29
mshA 575590 c.243T>C synonymous_variant 0.29
mshA 575593 c.246G>C synonymous_variant 0.22
mshA 575623 c.276C>G synonymous_variant 0.25
mshA 575629 c.282A>C synonymous_variant 0.29
mshA 575635 c.288A>C synonymous_variant 0.29
mshA 575638 c.291T>C synonymous_variant 0.29
mshA 575641 c.294A>G synonymous_variant 0.29
mshA 575648 p.Val101Gln missense_variant 0.29
mshA 575659 c.312A>G synonymous_variant 0.25
mshA 575665 c.318G>C synonymous_variant 0.25
rpoB 761414 c.1608A>G synonymous_variant 0.43
rpoB 761423 c.1617T>C synonymous_variant 0.38
rpoB 761435 c.1629T>C synonymous_variant 0.25
rpoB 761437 p.Ala544Asp missense_variant 0.25
rpoB 761439 p.Asp545Lys missense_variant 0.22
rpoB 761444 c.1638T>C synonymous_variant 0.33
rpoB 761447 c.1641C>G synonymous_variant 0.33
rpoB 761452 p.Val549Ala missense_variant 0.33
rpoB 761457 p.Pro551Ala missense_variant 0.33
rpoB 761462 c.1656C>G synonymous_variant 0.33
rpoB 761492 c.1686G>C synonymous_variant 0.3
rpoB 761510 c.1704T>C synonymous_variant 0.31
rpoB 761579 c.1773G>C synonymous_variant 0.15
rpoB 762011 c.2205G>C synonymous_variant 1.0
rpoB 762279 c.2474delA frameshift_variant 0.67
rpoB 762347 c.2541T>C synonymous_variant 0.4
rpoC 763456 c.87A>G synonymous_variant 0.25
rpoC 763468 c.99G>C synonymous_variant 0.29
rpoC 763486 c.117T>C synonymous_variant 0.33
rpoC 763528 c.159G>A synonymous_variant 0.33
rpoC 763570 c.201G>C synonymous_variant 0.22
rpoC 763807 c.438T>C synonymous_variant 0.22
rpoC 763819 c.450G>C synonymous_variant 0.25
rpoC 764577 p.Ser403Cys missense_variant 0.25
rpoC 764824 c.1455T>C synonymous_variant 0.4
rpoC 764830 c.1461C>G synonymous_variant 0.4
rpoC 764968 c.1599T>C synonymous_variant 0.29
rpoC 765613 p.His748Gln missense_variant 0.25
rpoC 765625 c.2256C>G synonymous_variant 0.29
rpoC 765628 c.2259G>C synonymous_variant 0.29
rpoC 765631 p.Asp754Glu missense_variant 0.25
rpoC 765658 c.2289C>T synonymous_variant 0.2
rpoC 765700 c.2331T>C synonymous_variant 0.25
rpoC 765734 c.2365T>C synonymous_variant 0.38
rpoC 765739 c.2370G>C synonymous_variant 0.44
rpoC 765751 c.2382C>G synonymous_variant 0.33
rpoC 765753 p.Asp795Ala missense_variant 0.33
rpoC 765772 c.2403C>G synonymous_variant 0.3
rpoC 765784 c.2415C>G synonymous_variant 0.33
rpoC 765796 c.2427C>T synonymous_variant 0.38
rpoC 765811 c.2442T>C synonymous_variant 0.38
rpoC 765814 c.2445A>G synonymous_variant 0.38
rpoC 765826 c.2457T>C synonymous_variant 0.44
rpoC 765835 c.2466C>T synonymous_variant 0.44
rpoC 765883 c.2514C>G synonymous_variant 0.43
rpoC 765886 c.2517C>G synonymous_variant 0.33
rpoC 765892 c.2523T>C synonymous_variant 0.33
rpoC 765928 c.2559C>G synonymous_variant 0.5
rpoC 765967 c.2598C>T synonymous_variant 0.5
rpoC 765970 c.2601C>T synonymous_variant 0.5
rpoC 765979 c.2610C>G synonymous_variant 0.5
rpoC 765982 c.2613C>T synonymous_variant 0.5
rpoC 765985 c.2616C>T synonymous_variant 0.5
rpoC 765994 c.2625A>T synonymous_variant 0.5
rpoC 767158 c.3789T>C synonymous_variant 0.4
mmpS5 778823 p.Ile28Thr missense_variant 1.0
fbiC 1303674 c.744C>G synonymous_variant 0.33
fbiC 1303686 c.756C>G synonymous_variant 0.33
fbiC 1303695 c.765T>C synonymous_variant 0.33
fbiC 1303708 c.778T>C synonymous_variant 0.33
fbiC 1304640 c.1710A>C synonymous_variant 1.0
Rv1258c 1406376 p.Gly322Val missense_variant 1.0
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.18
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.18
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.44
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.63
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.43
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.57
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.58
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.63
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.63
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.63
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.72
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.69
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.69
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.64
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.63
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.63
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.63
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.61
rrs 1472230 n.385C>T non_coding_transcript_exon_variant 0.19
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.61
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.61
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.63
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.59
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.5
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.4
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.36
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.33
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.33
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.4
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.5
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.71
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.71
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.71
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.65
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.65
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.65
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.68
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.71
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.71
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.71
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.71
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.68
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.62
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.62
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.72
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.74
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.79
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.77
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.79
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.75
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.77
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.8
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.8
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.8
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.8
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.8
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.82
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.56
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.6
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.55
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.55
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.55
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.5
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.5
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.5
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.46
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.46
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.46
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.46
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.46
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.46
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.5
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.46
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.46
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.43
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.38
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.43
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.29
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.2
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.33
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.2
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.2
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.2
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.2
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.4
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.78
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 0.88
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.88
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.88
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.86
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.86
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 0.88
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 0.88
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.88
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.88
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.91
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.96
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.95
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.96
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.96
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.95
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.74
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.95
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.96
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 0.98
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.98
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.98
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.98
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.97
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.97
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.97
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.97
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.97
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.97
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.97
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.97
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.97
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.95
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.94
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.94
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.94
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.93
rpsA 1833790 c.249T>A synonymous_variant 0.22
rpsA 1833799 c.258C>G synonymous_variant 0.22
rpsA 1833811 c.270G>C synonymous_variant 0.25
rpsA 1834097 c.556_557delTCinsAG synonymous_variant 0.33
rpsA 1834102 c.561T>C synonymous_variant 0.33
rpsA 1834222 c.681T>C synonymous_variant 0.29
rpsA 1834225 c.684C>G synonymous_variant 0.38
rpsA 1834240 c.699T>C synonymous_variant 0.29
rpsA 1834249 c.708T>C synonymous_variant 0.29
rpsA 1834261 c.720A>C synonymous_variant 0.29
rpsA 1834264 c.723G>C synonymous_variant 0.29
rpsA 1834297 c.756C>G synonymous_variant 0.4
rpsA 1834303 c.762T>G synonymous_variant 0.4
rpsA 1834306 c.765T>C synonymous_variant 0.33
rpsA 1834348 c.807T>C synonymous_variant 0.5
rpsA 1834366 c.825A>G synonymous_variant 0.4
rpsA 1834411 c.870T>C synonymous_variant 0.29
rpsA 1834417 c.876G>C synonymous_variant 0.29
rpsA 1834423 c.882G>C synonymous_variant 0.29
rpsA 1834435 c.894G>C synonymous_variant 0.29
rpsA 1834451 c.910T>C synonymous_variant 0.29
rpsA 1834465 c.924T>C synonymous_variant 0.4
rpsA 1834468 c.927A>G synonymous_variant 0.33
rpsA 1834474 c.933C>G synonymous_variant 0.33
PPE35 2169882 p.Ser244Ile missense_variant 1.0
eis 2714940 c.392delA frameshift_variant 1.0
thyA 3073925 c.547T>C synonymous_variant 0.33
thyA 3073926 c.546G>C synonymous_variant 0.33
thyA 3073929 c.543T>C synonymous_variant 0.33
ald 3087311 c.492C>G synonymous_variant 1.0
fbiB 3642465 p.Asp311His missense_variant 1.0
alr 3840300 p.Pro374His missense_variant 1.0
rpoA 3877542 c.966C>T synonymous_variant 0.25
rpoA 3877553 p.Glu319Gln missense_variant 0.25
rpoA 3877557 c.951C>G synonymous_variant 0.25
rpoA 3877587 c.921A>G synonymous_variant 0.22
rpoA 3877613 p.Ile299Val missense_variant 0.25
rpoA 3877638 c.870T>C synonymous_variant 0.25
rpoA 3877656 c.852T>C synonymous_variant 0.25
rpoA 3878288 p.Thr74Pro missense_variant 1.0
clpC1 4038271 p.Pro812Ala missense_variant 0.22
clpC1 4038272 p.Gly811Ser missense_variant 0.22
clpC1 4038278 c.2427T>C synonymous_variant 0.22
clpC1 4038293 c.2412G>C synonymous_variant 0.22
clpC1 4038302 c.2403C>G synonymous_variant 0.2
clpC1 4038308 p.Val799Ile missense_variant 0.2
clpC1 4038317 c.2388G>C synonymous_variant 0.22
clpC1 4038347 c.2358G>C synonymous_variant 0.25
clpC1 4038356 c.2349T>C synonymous_variant 0.33
clpC1 4038878 c.1827A>G synonymous_variant 0.22
clpC1 4038908 c.1797C>G synonymous_variant 0.18
clpC1 4038914 c.1791G>C synonymous_variant 0.18
clpC1 4038923 c.1782A>G synonymous_variant 0.18
clpC1 4038932 c.1773G>C synonymous_variant 0.2
clpC1 4038953 c.1752A>G synonymous_variant 0.22
clpC1 4038956 c.1749T>C synonymous_variant 0.22
clpC1 4038965 c.1740T>C synonymous_variant 0.2
clpC1 4038971 c.1734T>C synonymous_variant 0.2
clpC1 4038974 c.1731T>C synonymous_variant 0.2
clpC1 4038989 c.1716T>C synonymous_variant 0.27
clpC1 4038997 c.1708T>C synonymous_variant 0.27
clpC1 4039022 c.1683A>G synonymous_variant 0.27
clpC1 4039073 c.1632C>G synonymous_variant 0.43
clpC1 4039085 c.1620A>G synonymous_variant 0.38
clpC1 4039090 c.1615C>T synonymous_variant 0.38
clpC1 4039097 c.1608G>C synonymous_variant 0.33
clpC1 4039103 c.1602T>C synonymous_variant 0.25
clpC1 4039106 c.1599G>C synonymous_variant 0.25
clpC1 4039112 c.1593C>G synonymous_variant 0.38
clpC1 4039121 c.1584T>C synonymous_variant 0.38
clpC1 4039124 c.1581C>G synonymous_variant 0.38
clpC1 4039142 c.1563A>G synonymous_variant 0.29
clpC1 4039145 c.1560G>C synonymous_variant 0.29
clpC1 4039169 p.Glu512Asp missense_variant 0.33
clpC1 4039172 c.1533A>G synonymous_variant 0.33
clpC1 4039178 c.1527G>C synonymous_variant 0.29
clpC1 4039183 c.1522T>C synonymous_variant 0.29
clpC1 4039187 c.1518G>C synonymous_variant 0.29
clpC1 4039190 c.1515C>G synonymous_variant 0.29
clpC1 4039208 c.1497C>G synonymous_variant 0.29
clpC1 4039415 c.1289dupA frameshift_variant 0.88
clpC1 4040792 c.-88A>T upstream_gene_variant 1.0
embC 4241168 p.Leu436Val missense_variant 0.33
embA 4243235 c.3G>T synonymous_variant 1.0