TB-Profiler result

Run: SRR13861400
Summary

Run ID: SRR13861400

Sample name:

Date: 03-04-2023 09:30:55

Number of reads: 1561918

Percentage reads mapped: 52.11

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 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.46 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 7697 c.396C>G synonymous_variant 0.15
gyrA 7760 c.459C>T synonymous_variant 0.15
gyrA 7763 c.462T>C synonymous_variant 0.15
gyrA 7799 c.498A>G synonymous_variant 0.17
gyrA 7835 c.534A>G synonymous_variant 0.17
gyrA 7838 c.537C>G synonymous_variant 0.14
gyrA 8399 c.1098T>C synonymous_variant 0.14
gyrA 8597 c.1296C>G synonymous_variant 0.14
gyrA 8603 c.1302A>G synonymous_variant 0.16
gyrA 8619 c.1318T>C synonymous_variant 0.16
gyrA 8624 c.1323G>C synonymous_variant 0.15
gyrA 8627 c.1326C>G synonymous_variant 0.15
gyrA 8636 c.1335A>G synonymous_variant 0.17
gyrA 8642 c.1341A>G synonymous_variant 0.18
gyrA 8645 c.1344C>G synonymous_variant 0.18
gyrA 8672 c.1371A>G synonymous_variant 0.18
gyrA 8693 c.1392T>C synonymous_variant 0.15
gyrA 8699 c.1398A>G synonymous_variant 0.17
gyrA 8711 c.1410A>C synonymous_variant 0.15
gyrA 8714 c.1413A>G synonymous_variant 0.15
gyrA 8717 c.1416C>G synonymous_variant 0.15
gyrA 8720 c.1419G>A synonymous_variant 0.15
gyrA 8729 c.1428T>C synonymous_variant 0.16
gyrA 8732 c.1431G>C synonymous_variant 0.16
gyrA 8747 c.1446A>G synonymous_variant 0.15
gyrA 8762 c.1461G>C synonymous_variant 0.14
gyrA 8765 p.Asp488Glu missense_variant 0.16
gyrA 8767 p.Arg489Lys missense_variant 0.15
gyrA 8780 p.Asp493Glu missense_variant 0.15
gyrA 8786 c.1485T>C synonymous_variant 0.14
gyrA 8796 p.Ile499Val missense_variant 0.16
gyrA 8801 c.1500G>C synonymous_variant 0.16
gyrA 8810 c.1509A>C synonymous_variant 0.17
gyrA 8816 c.1515C>T synonymous_variant 0.15
gyrA 8880 p.Lys527Gln missense_variant 0.94
mshA 575713 c.366G>A synonymous_variant 0.13
mshA 575719 c.372C>T synonymous_variant 0.13
mshA 575752 c.405G>A synonymous_variant 0.12
rpoB 760181 c.375T>C synonymous_variant 0.15
rpoB 760184 c.378A>G synonymous_variant 0.14
rpoB 760223 c.417T>C synonymous_variant 0.15
rpoB 760235 c.429T>C synonymous_variant 0.15
rpoB 760307 c.501T>C synonymous_variant 0.16
rpoB 760328 c.522G>C synonymous_variant 0.15
rpoB 760337 c.531C>G synonymous_variant 0.16
rpoB 760340 c.534G>C synonymous_variant 0.16
rpoB 760361 c.555T>C synonymous_variant 0.19
rpoB 760406 c.600G>C synonymous_variant 0.16
rpoB 760418 c.612G>C synonymous_variant 0.19
rpoB 760424 c.618C>G synonymous_variant 0.19
rpoB 760430 c.624T>C synonymous_variant 0.2
rpoB 760514 c.708C>T synonymous_variant 0.13
rpoB 760533 p.Val243Thr missense_variant 0.13
rpoB 760547 c.741G>C synonymous_variant 0.14
rpoB 760972 p.Arg389Leu missense_variant 0.9
rpoB 762218 c.2412T>G synonymous_variant 0.14
rpoB 762254 c.2448T>C synonymous_variant 0.15
rpoB 762266 c.2460T>C synonymous_variant 0.16
rpoB 762284 c.2478G>C synonymous_variant 0.17
rpoB 762293 c.2487T>C synonymous_variant 0.17
rpoB 762317 c.2511A>G synonymous_variant 0.18
rpoB 762329 c.2523G>C synonymous_variant 0.16
rpoB 762338 c.2532T>C synonymous_variant 0.14
rpoC 763945 c.576T>C synonymous_variant 0.14
rpoC 763960 c.591T>C synonymous_variant 0.18
rpoC 763967 p.Gly200Ser missense_variant 0.15
rpoC 765111 p.Met581Lys missense_variant 0.96
rpoC 765161 p.Glu598Lys missense_variant 1.0
rpoC 765404 p.Leu679Val missense_variant 0.15
rpoC 765540 p.Ala724Val missense_variant 0.88
rpoC 766390 c.3021C>T synonymous_variant 0.15
rpoC 766408 c.3039C>T synonymous_variant 0.15
rpoC 766426 c.3057C>T synonymous_variant 0.16
rpoC 766483 c.3114G>C synonymous_variant 0.14
rpoC 766486 c.3117A>C synonymous_variant 0.14
rpoC 766495 c.3126C>T synonymous_variant 0.13
rpoC 767068 c.3699G>T synonymous_variant 0.94
mmpR5 778439 c.-551C>A upstream_gene_variant 1.0
rplC 801357 p.His183Gln missense_variant 1.0
fbiC 1303911 c.981G>C synonymous_variant 0.14
fbiC 1304229 c.1301delC frameshift_variant 1.0
fbiC 1304832 c.1902C>G synonymous_variant 0.13
fbiC 1304853 c.1923C>G synonymous_variant 0.15
fbiC 1304856 c.1926C>G synonymous_variant 0.15
fbiC 1304872 c.1942_1944delAGCinsTCG synonymous_variant 0.15
fbiC 1304877 c.1947T>C synonymous_variant 0.15
fbiC 1304878 c.1948_1950delCGCinsAGG synonymous_variant 0.15
fbiC 1304893 p.Gly655Ser missense_variant 0.15
fbiC 1305331 p.Glu801Asn missense_variant 0.14
rrs 1472044 n.199G>C non_coding_transcript_exon_variant 0.15
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.16
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.16
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.18
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.13
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.23
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.22
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.28
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.28
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.32
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.31
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.31
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.31
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.31
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.32
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.31
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.31
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.32
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.33
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.32
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.32
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.33
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.33
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.27
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.23
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.19
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.16
rrs 1472288 n.444delT non_coding_transcript_exon_variant 0.89
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.15
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.31
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.32
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.31
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.29
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.29
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.29
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.28
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.28
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.28
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.28
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.28
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.27
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.26
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.28
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.4
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.45
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.48
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.45
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.43
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.43
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.44
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.45
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.44
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.46
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.47
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.47
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.21
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.14
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.14
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.14
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.16
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.15
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.16
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.16
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.13
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.17
rrl 1475015 n.1358C>T non_coding_transcript_exon_variant 0.17
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.17
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.17
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.18
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.18
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.18
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.14
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.2
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.19
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.14
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.19
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.18
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.18
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.18
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.18
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.16
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.17
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.13
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.3
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.35
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.46
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.46
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.46
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.46
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.45
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.45
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.46
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.46
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.46
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.46
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.46
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.47
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.48
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.48
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.49
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.5
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.63
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.74
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.74
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.73
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.72
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.71
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.6
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.7
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.73
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.73
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.73
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.74
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.72
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.57
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.49
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.46
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.46
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.48
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.48
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.47
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.48
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.48
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.47
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.47
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.45
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.42
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.42
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.42
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.46
inhA 1674756 c.555T>C synonymous_variant 0.15
rpsA 1834222 c.681T>C synonymous_variant 0.14
rpsA 1834225 c.684C>G synonymous_variant 0.15
rpsA 1834240 c.699T>C synonymous_variant 0.18
rpsA 1834249 c.708T>C synonymous_variant 0.2
rpsA 1834261 c.720A>C synonymous_variant 0.19
rpsA 1834264 c.723G>C synonymous_variant 0.2
rpsA 1834297 c.756C>G synonymous_variant 0.18
rpsA 1834303 c.762T>G synonymous_variant 0.17
rpsA 1834306 c.765T>C synonymous_variant 0.17
rpsA 1834348 c.807T>C synonymous_variant 0.16
rpsA 1834366 c.825A>G synonymous_variant 0.16
rpsA 1834375 c.834G>A synonymous_variant 0.14
rpsA 1834396 c.855G>C synonymous_variant 0.15
rpsA 1834417 c.876G>C synonymous_variant 0.14
rpsA 1834423 c.882G>C synonymous_variant 0.14
rpsA 1834435 c.894G>C synonymous_variant 0.14
rpsA 1834474 c.933C>G synonymous_variant 0.14
rpsA 1834489 c.948T>C synonymous_variant 0.15
rpsA 1834498 c.957C>T synonymous_variant 0.15
tlyA 1917989 p.Ala17Gly missense_variant 0.98
ndh 2102525 p.Phe173Tyr missense_variant 0.98
ndh 2102538 c.504_505insT frameshift_variant 0.98
Rv1979c 2222978 p.Ile63Phe missense_variant 1.0
Rv1979c 2223052 p.Glu38Val missense_variant 1.0
pncA 2289415 c.-174C>G upstream_gene_variant 1.0
kasA 2518057 c.-58A>C upstream_gene_variant 1.0
kasA 2518799 p.Pro229Ser missense_variant 0.94
eis 2714983 p.Ala117Glu missense_variant 1.0
thyX 3067304 c.642A>G synonymous_variant 0.15
thyX 3067316 c.630A>G synonymous_variant 0.16
thyX 3067325 c.621A>G synonymous_variant 0.15
thyX 3067355 c.591A>C synonymous_variant 0.17
thyX 3067367 c.579G>C synonymous_variant 0.16
thyX 3067376 c.570G>C synonymous_variant 0.17
thyX 3067391 c.555G>C synonymous_variant 0.16
thyX 3067394 c.552G>C synonymous_variant 0.15
thyX 3067412 c.534C>G synonymous_variant 0.18
thyX 3067439 c.507A>G synonymous_variant 0.19
thyX 3067445 c.501C>G synonymous_variant 0.18
thyX 3067451 c.495G>A synonymous_variant 0.18
thyX 3067457 c.489C>G synonymous_variant 0.17
thyX 3067463 p.Ile161Val missense_variant 0.16
thyX 3067466 c.480G>C synonymous_variant 0.16
thyX 3067470 p.Asn159Ser missense_variant 0.15
thyX 3067493 c.453A>G synonymous_variant 0.16
thyX 3067500 p.Lys149Arg missense_variant 0.17
thyX 3067515 p.Ser144Thr missense_variant 0.14
fbiA 3640404 c.-139C>A upstream_gene_variant 1.0
fbiB 3642056 c.522C>G synonymous_variant 1.0
rpoA 3877967 p.Thr181Ser missense_variant 0.92
rpoA 3877972 c.535delG frameshift_variant 0.93
rpoA 3878061 c.447G>C synonymous_variant 0.16
rpoA 3878067 c.441C>G synonymous_variant 0.16
rpoA 3878070 c.438T>C synonymous_variant 0.16
rpoA 3878082 c.426T>C synonymous_variant 0.14
clpC1 4038748 p.Arg653Cys missense_variant 0.14
clpC1 4039517 c.1188C>G synonymous_variant 0.15
clpC1 4039524 p.Phe394Tyr missense_variant 0.15
clpC1 4039547 c.1158C>G synonymous_variant 0.17
clpC1 4039553 c.1152C>G synonymous_variant 0.17
clpC1 4039562 c.1143C>G synonymous_variant 0.17
clpC1 4039565 c.1140G>C synonymous_variant 0.17
clpC1 4039576 p.Ala377Ser missense_variant 0.14
clpC1 4039586 c.1119G>C synonymous_variant 0.16
clpC1 4039610 c.1095G>C synonymous_variant 0.15
clpC1 4039616 c.1089G>C synonymous_variant 0.15
clpC1 4039622 c.1083C>G synonymous_variant 0.15
clpC1 4039682 c.1023C>G synonymous_variant 0.17
clpC1 4039685 c.1020C>T synonymous_variant 0.16
clpC1 4039694 c.1011G>C synonymous_variant 0.14
clpC1 4039724 c.981A>G synonymous_variant 0.18
clpC1 4039777 c.927_928insG frameshift_variant 1.0
clpC1 4039789 p.Ser306Thr missense_variant 0.13
clpC1 4040363 c.342A>C synonymous_variant 0.14
clpC1 4040369 c.336C>G synonymous_variant 0.14
embB 4247545 p.Ser344Arg missense_variant 0.94
aftB 4268812 p.Ser9Pro missense_variant 1.0