TB-Profiler result

Run: SRR13861251
Summary

Run ID: SRR13861251

Sample name:

Date: 03-04-2023 09:27:10

Number of reads: 296173

Percentage reads mapped: 14.82

Strain: lineage4.9

Drug-resistance: RR-TB

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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
rpoB 761135 p.Leu443Phe missense_variant 0.18 rifampicin
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 7427 c.126G>C synonymous_variant 0.2
gyrA 7442 c.141G>C synonymous_variant 0.18
gyrA 7451 c.150C>G synonymous_variant 0.18
gyrA 7457 c.156T>C synonymous_variant 0.18
gyrA 7466 c.165G>A synonymous_variant 0.18
gyrA 7469 c.168C>T synonymous_variant 0.18
gyrA 7472 c.171T>C synonymous_variant 0.18
gyrA 7475 c.174A>C synonymous_variant 0.18
gyrA 7480 p.Phe60Tyr missense_variant 0.17
gyrA 7484 c.183T>C synonymous_variant 0.17
gyrA 7487 c.186C>G synonymous_variant 0.15
gyrA 7490 c.189C>T synonymous_variant 0.15
gyrA 7523 c.222C>G synonymous_variant 0.17
gyrA 7532 c.231T>C synonymous_variant 0.17
gyrA 7541 c.240C>G synonymous_variant 0.17
gyrA 7697 c.396C>G synonymous_variant 0.12
gyrA 8711 c.1410A>C synonymous_variant 0.25
gyrA 8714 c.1413A>G synonymous_variant 0.25
gyrA 8717 c.1416C>G synonymous_variant 0.25
gyrA 8720 c.1419G>A synonymous_variant 0.25
gyrA 8729 c.1428T>C synonymous_variant 0.22
gyrA 8732 c.1431G>C synonymous_variant 0.22
gyrA 8747 c.1446A>G synonymous_variant 0.25
gyrA 8756 c.1455A>G synonymous_variant 0.25
gyrA 8762 c.1461G>C synonymous_variant 0.25
gyrA 8765 p.Asp488Glu missense_variant 0.22
gyrA 8767 p.Arg489Lys missense_variant 0.22
gyrA 8880 p.Lys527Gln missense_variant 1.0
gyrA 9305 c.2004C>G synonymous_variant 0.18
fgd1 491094 c.312C>G synonymous_variant 0.18
fgd1 491106 c.324T>C synonymous_variant 0.18
fgd1 491121 c.339A>G synonymous_variant 0.13
fgd1 491137 p.Glu119Gln missense_variant 0.2
fgd1 491144 p.Ala121Glu missense_variant 0.2
fgd1 491166 c.384G>C synonymous_variant 0.15
fgd1 491181 c.399T>C synonymous_variant 0.14
fgd1 491191 p.Gly137Arg missense_variant 0.14
fgd1 491194 c.412_414delCTAinsTTG synonymous_variant 0.13
fgd1 491202 c.420G>C synonymous_variant 0.13
fgd1 491203 p.Gln141Glu missense_variant 0.13
fgd1 491212 p.Ser144Arg missense_variant 0.12
fgd1 491217 c.435T>C synonymous_variant 0.12
fgd1 491241 p.Asp153Glu missense_variant 0.16
fgd1 491259 c.477T>C synonymous_variant 0.12
rpoB 760475 c.669A>G synonymous_variant 0.15
rpoB 760481 c.675G>C synonymous_variant 0.14
rpoB 760514 c.708C>T synonymous_variant 0.13
rpoB 760522 p.Ser239Asn missense_variant 0.14
rpoB 760972 p.Arg389Leu missense_variant 1.0
rpoB 761150 c.1344A>C synonymous_variant 0.18
rpoB 761165 c.1359G>C synonymous_variant 0.2
rpoB 761168 c.1362C>G synonymous_variant 0.2
rpoB 761171 c.1365C>T synonymous_variant 0.22
rpoB 761180 c.1374A>C synonymous_variant 0.22
rpoB 761222 c.1416G>C synonymous_variant 0.15
rpoB 761249 c.1443A>G synonymous_variant 0.15
rpoB 761255 c.1449T>G synonymous_variant 0.15
rpoB 761261 c.1455G>T synonymous_variant 0.18
rpoB 761327 c.1521A>G synonymous_variant 0.15
rpoC 763158 c.-212C>T upstream_gene_variant 0.15
rpoC 763444 c.75T>C synonymous_variant 0.12
rpoC 763528 c.159G>A synonymous_variant 0.12
rpoC 763570 c.201G>C synonymous_variant 0.13
rpoC 763888 c.519G>C synonymous_variant 0.14
rpoC 764380 c.1011G>C synonymous_variant 0.2
rpoC 764381 c.1012_1013delTCinsAG synonymous_variant 0.2
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.2
rpoC 764405 c.1036A>C synonymous_variant 0.17
rpoC 764434 c.1065A>G synonymous_variant 0.15
rpoC 764446 c.1077T>C synonymous_variant 0.15
rpoC 764449 c.1080G>C synonymous_variant 0.15
rpoC 764455 c.1086G>C synonymous_variant 0.14
rpoC 764461 c.1092A>G synonymous_variant 0.15
rpoC 764497 c.1128A>G synonymous_variant 0.18
rpoC 764521 c.1152T>C synonymous_variant 0.14
rpoC 764530 c.1161C>G synonymous_variant 0.15
rpoC 764536 c.1167G>C synonymous_variant 0.15
rpoC 764539 c.1170C>G synonymous_variant 0.15
rpoC 764560 c.1191T>C synonymous_variant 0.17
rpoC 764566 c.1197C>G synonymous_variant 0.18
rpoC 764573 c.1204_1206delCTTinsTTG synonymous_variant 0.18
rpoC 764576 c.1207_1208delTCinsAG synonymous_variant 0.18
rpoC 764581 c.1212T>C synonymous_variant 0.15
rpoC 764626 c.1257C>T synonymous_variant 0.13
rpoC 764632 c.1263T>C synonymous_variant 0.13
rpoC 764764 c.1395T>C synonymous_variant 0.12
rpoC 764809 c.1440C>T synonymous_variant 0.13
rpoC 764812 c.1443C>G synonymous_variant 0.13
rpoC 764824 c.1455T>C synonymous_variant 0.19
rpoC 764830 c.1461C>G synonymous_variant 0.15
rpoC 764858 c.1489T>C synonymous_variant 0.15
rpoC 764872 c.1503A>G synonymous_variant 0.17
rpoC 764893 c.1524T>C synonymous_variant 0.15
rpoC 764911 c.1542A>G synonymous_variant 0.27
rpoC 764923 c.1554A>G synonymous_variant 0.27
rpoC 764932 c.1563C>A synonymous_variant 0.27
rpoC 764968 c.1599T>C synonymous_variant 0.27
rpoC 764995 c.1626C>G synonymous_variant 0.2
rpoC 765007 c.1638T>G synonymous_variant 0.2
rpoC 765019 c.1650A>G synonymous_variant 0.18
rpoC 765022 c.1653G>C synonymous_variant 0.2
rpoC 765034 c.1665T>C synonymous_variant 0.22
rpoC 765040 c.1671T>C synonymous_variant 0.22
rpoC 765041 c.1672T>C synonymous_variant 0.22
rpoC 765047 c.1678T>C synonymous_variant 0.22
rpoC 765111 p.Met581Lys missense_variant 1.0
rpoC 765161 p.Glu598Lys missense_variant 1.0
rpoC 765331 p.Ser654Arg missense_variant 0.14
rpoC 765540 p.Ala724Val missense_variant 1.0
rpoC 766978 c.3609C>G synonymous_variant 0.22
rpoC 767068 c.3699G>T synonymous_variant 0.89
rpoC 767074 c.3705T>C synonymous_variant 0.2
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 0.17
fbiC 1303914 c.984C>G synonymous_variant 0.17
fbiC 1303920 c.990C>G synonymous_variant 0.18
fbiC 1303923 c.993C>T synonymous_variant 0.18
fbiC 1303929 c.999G>C synonymous_variant 0.17
fbiC 1303947 c.1017T>C synonymous_variant 0.17
fbiC 1303948 p.Gly340Arg missense_variant 0.17
fbiC 1303969 p.Val347Ile missense_variant 0.17
fbiC 1303995 c.1065C>T synonymous_variant 0.14
fbiC 1304001 c.1071C>G synonymous_variant 0.14
fbiC 1304008 c.1078T>C synonymous_variant 0.15
fbiC 1304229 c.1301delC frameshift_variant 1.0
fbiC 1304703 c.1773C>G synonymous_variant 0.15
fbiC 1304715 c.1785G>C synonymous_variant 0.2
fbiC 1304724 c.1794A>G synonymous_variant 0.2
fbiC 1304727 c.1797A>G synonymous_variant 0.2
fbiC 1304742 c.1812T>C synonymous_variant 0.17
fbiC 1304748 c.1818T>C synonymous_variant 0.15
fbiC 1304754 c.1824G>A synonymous_variant 0.15
fbiC 1304757 c.1827A>G synonymous_variant 0.15
fbiC 1304787 c.1857T>C synonymous_variant 0.13
fbiC 1304790 c.1860C>G synonymous_variant 0.13
rrs 1472288 n.444delT non_coding_transcript_exon_variant 1.0
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.14
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.15
tlyA 1917989 p.Ala17Gly missense_variant 1.0
ndh 2102525 p.Phe173Tyr missense_variant 1.0
ndh 2102538 c.504_505insT frameshift_variant 1.0
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 0.88
eis 2714983 p.Ala117Glu missense_variant 1.0
folC 2747394 p.Ile69Val missense_variant 0.2
folC 2747395 c.204T>C synonymous_variant 0.2
folC 2747401 c.198G>C synonymous_variant 0.18
folC 2747407 c.192T>C synonymous_variant 0.18
folC 2747411 p.Ser63Ala missense_variant 0.18
folC 2747416 c.183A>G synonymous_variant 0.2
folC 2747419 c.180C>G synonymous_variant 0.22
folC 2747430 c.169C>T synonymous_variant 0.25
folC 2747439 p.Met54Leu missense_variant 0.17
folC 2747442 c.157T>C synonymous_variant 0.17
folC 2747443 c.156G>A synonymous_variant 0.17
thyX 3067316 c.630A>G synonymous_variant 0.2
thyX 3067325 c.621A>G synonymous_variant 0.2
thyX 3067355 c.591A>C synonymous_variant 0.18
thyX 3067367 c.579G>C synonymous_variant 0.22
thyX 3067376 c.570G>C synonymous_variant 0.18
thyX 3067391 c.555G>C synonymous_variant 0.21
thyX 3067394 c.552G>C synonymous_variant 0.21
thyX 3067412 c.534C>G synonymous_variant 0.21
thyX 3067439 c.507A>G synonymous_variant 0.2
thyX 3067445 c.501C>G synonymous_variant 0.19
thyX 3067451 c.495G>A synonymous_variant 0.18
thyX 3067457 c.489C>G synonymous_variant 0.19
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 1.0
rpoA 3877972 c.535delG frameshift_variant 1.0
rpoA 3878284 p.Glu75Ala missense_variant 0.2
rpoA 3878292 c.216T>C synonymous_variant 0.18
rpoA 3878298 c.210A>G synonymous_variant 0.18
rpoA 3878304 c.204G>C synonymous_variant 0.2
rpoA 3878313 c.195G>C synonymous_variant 0.2
rpoA 3878322 c.186A>G synonymous_variant 0.22
rpoA 3878331 c.177A>G synonymous_variant 0.2
rpoA 3878334 c.174T>C synonymous_variant 0.22
rpoA 3878337 c.171T>C synonymous_variant 0.22
rpoA 3878346 c.162T>C synonymous_variant 0.22
clpC1 4038271 p.Pro812Ala missense_variant 0.17
clpC1 4038272 p.Gly811Ser missense_variant 0.17
clpC1 4038278 c.2427T>C synonymous_variant 0.17
clpC1 4038293 c.2412G>C synonymous_variant 0.18
clpC1 4038302 c.2403C>G synonymous_variant 0.18
clpC1 4038308 p.Val799Ile missense_variant 0.17
clpC1 4038317 c.2388G>C synonymous_variant 0.15
clpC1 4038347 c.2358G>C synonymous_variant 0.2
clpC1 4038356 c.2349T>C synonymous_variant 0.22
clpC1 4038359 c.2346A>G synonymous_variant 0.25
clpC1 4038368 c.2337T>C synonymous_variant 0.3
clpC1 4038388 c.2317T>C synonymous_variant 0.2
clpC1 4038398 c.2307G>T synonymous_variant 0.18
clpC1 4038498 p.Ser736Thr missense_variant 0.15
clpC1 4038790 c.1915C>T synonymous_variant 0.15
clpC1 4038812 c.1893T>C synonymous_variant 0.18
clpC1 4038815 c.1890G>T synonymous_variant 0.17
clpC1 4038851 c.1854G>A synonymous_variant 0.18
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 0.25
clpC1 4038923 c.1782A>G synonymous_variant 0.22
clpC1 4038932 c.1773G>C synonymous_variant 0.22
clpC1 4039777 c.927_928insG frameshift_variant 1.0
embB 4247545 p.Ser344Arg missense_variant 1.0
embB 4248206 p.Ser565Gly missense_variant 0.19
embB 4248220 c.1707A>G synonymous_variant 0.19
embB 4248241 c.1728C>T synonymous_variant 0.24
embB 4248265 c.1752C>T synonymous_variant 0.25
embB 4248266 c.1753C>T synonymous_variant 0.25
embB 4248277 c.1764G>C synonymous_variant 0.25
embB 4248304 c.1791G>T synonymous_variant 0.31
embB 4248316 c.1803C>G synonymous_variant 0.21
embB 4248319 c.1806A>G synonymous_variant 0.21
embB 4248322 c.1809G>C synonymous_variant 0.21
embB 4248343 c.1830G>C synonymous_variant 0.14
embB 4248346 c.1833G>C synonymous_variant 0.14
embB 4248350 c.1837T>C synonymous_variant 0.13
embB 4248355 c.1842A>G synonymous_variant 0.13
embB 4248358 c.1845C>G synonymous_variant 0.13
embB 4248361 c.1848A>G synonymous_variant 0.13
embB 4248362 p.Ser617Ala missense_variant 0.13
aftB 4267580 c.1257G>C synonymous_variant 0.12
aftB 4268812 p.Ser9Pro missense_variant 1.0