TB-Profiler result

Run: ERR4813861
Summary

Run ID: ERR4813861

Sample name:

Date: 01-04-2023 13:02:23

Number of reads: 3005541

Percentage reads mapped: 93.5

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
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 1472307 n.462C>T non_coding_transcript_exon_variant 0.15 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7538 c.237G>A synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7607 c.306C>G synonymous_variant 0.13
gyrA 8040 p.Gly247Ser missense_variant 0.97
gyrA 8198 c.897T>C synonymous_variant 0.13
gyrA 8207 c.906T>C synonymous_variant 0.14
gyrA 8225 c.924T>C synonymous_variant 0.13
gyrA 8234 c.933T>G synonymous_variant 0.13
gyrA 8399 c.1098T>C synonymous_variant 0.14
gyrA 8420 c.1119T>C synonymous_variant 0.15
gyrA 8423 c.1122G>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 0.13
rpoB 761222 c.1416G>C synonymous_variant 0.15
rpoB 761249 c.1443A>G synonymous_variant 0.14
rpoB 761255 c.1449T>G synonymous_variant 0.16
rpoB 761261 c.1455G>T synonymous_variant 0.17
rpoB 761492 c.1686G>C synonymous_variant 0.14
rpoB 761531 c.1725C>G synonymous_variant 0.15
rpoC 762989 c.-381G>C upstream_gene_variant 0.14
rpoC 762995 c.-375G>T upstream_gene_variant 0.13
rpoC 763040 c.-330C>G upstream_gene_variant 0.14
rpoC 763070 c.-300T>C upstream_gene_variant 0.15
rpoC 763076 c.-294C>G upstream_gene_variant 0.16
rpoC 763085 c.-285C>G upstream_gene_variant 0.14
rpoC 763528 c.159G>A synonymous_variant 0.14
rpoC 763594 c.225C>T synonymous_variant 0.16
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765700 c.2331T>C synonymous_variant 0.16
rpoC 765772 c.2403C>G synonymous_variant 0.15
rpoC 765784 c.2415C>G synonymous_variant 0.17
rpoC 765796 c.2427C>T synonymous_variant 0.18
rpoC 765811 c.2442T>C synonymous_variant 0.15
rpoC 765814 c.2445A>G synonymous_variant 0.14
rpoC 765835 c.2466C>T synonymous_variant 0.12
rpoC 766804 c.3435A>G synonymous_variant 0.14
rpoC 766933 c.3564A>G synonymous_variant 0.15
rpoC 766945 c.3576A>G synonymous_variant 0.15
rpoC 766963 c.3594T>C synonymous_variant 0.14
rpoC 766972 c.3603G>C synonymous_variant 0.16
rpoC 766978 c.3609C>G synonymous_variant 0.16
rpoC 766996 c.3627C>T synonymous_variant 0.16
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.16
rpoC 767014 c.3645G>C synonymous_variant 0.17
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.17
rpoC 767059 c.3690T>G synonymous_variant 0.17
rpoC 767062 c.3693C>A synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779033 p.Asp15Ala missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781682 c.123T>C synonymous_variant 0.14
rpsL 781715 c.156T>C synonymous_variant 0.13
rpsL 781793 c.234G>C synonymous_variant 0.13
rpsL 781859 c.300T>C synonymous_variant 0.14
rpsL 781868 c.309T>C synonymous_variant 0.13
rpsL 781871 c.312G>C synonymous_variant 0.14
rpsL 781892 c.333A>G synonymous_variant 0.14
rpsL 781898 c.339A>T synonymous_variant 0.14
fbiC 1303947 c.1017T>C synonymous_variant 0.14
fbiC 1303948 p.Gly340Arg missense_variant 0.14
fbiC 1303969 p.Val347Ile missense_variant 0.17
fbiC 1303973 p.Gly348Ala missense_variant 0.17
fbiC 1303981 p.Val351Ile missense_variant 0.19
fbiC 1303995 c.1065C>T synonymous_variant 0.18
fbiC 1304001 c.1071C>G synonymous_variant 0.16
fbiC 1304008 c.1078T>C synonymous_variant 0.14
fbiC 1304580 c.1650T>C synonymous_variant 0.13
fbiC 1304634 c.1704C>G synonymous_variant 0.14
fbiC 1304640 c.1710A>C synonymous_variant 0.16
fbiC 1304646 c.1716T>C synonymous_variant 0.16
fbiC 1304658 c.1728C>G synonymous_variant 0.15
fbiC 1304670 c.1740G>T synonymous_variant 0.13
fbiC 1304703 c.1773C>G synonymous_variant 0.14
fbiC 1304715 c.1785G>C synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.16
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.16
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.17
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.18
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.13
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.16
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.2
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.2
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.2
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.18
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.19
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.17
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 0.17
rrl 1474962 n.1306delG non_coding_transcript_exon_variant 0.18
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.19
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.19
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.18
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.15
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.12
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.14
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.15
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.15
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.19
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.18
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.16
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.15
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.16
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.14
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.14
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.14
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.14
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.88
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.13
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.15
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.13
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169834 p.Gly260Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.97
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449390 p.Arg296Leu missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877953 c.555G>A synonymous_variant 0.14
rpoA 3877962 c.546G>T synonymous_variant 0.14
rpoA 3878271 c.237T>C synonymous_variant 0.14
rpoA 3878284 p.Glu75Ala missense_variant 0.15
rpoA 3878292 c.216T>C synonymous_variant 0.16
rpoA 3878298 c.210A>G synonymous_variant 0.15
rpoA 3878304 c.204G>C synonymous_variant 0.15
rpoA 3878313 c.195G>C synonymous_variant 0.15
rpoA 3878322 c.186A>G synonymous_variant 0.15
rpoA 3878331 c.177A>G synonymous_variant 0.16
rpoA 3878334 c.174T>C synonymous_variant 0.16
rpoA 3878337 c.171T>C synonymous_variant 0.15
rpoA 3878346 c.162T>C synonymous_variant 0.16
rpoA 3878364 c.144A>G synonymous_variant 0.16
rpoA 3878367 c.141C>G synonymous_variant 0.15
rpoA 3878370 c.138T>C synonymous_variant 0.16
rpoA 3878376 c.132G>C synonymous_variant 0.17
rpoA 3878385 c.123C>G synonymous_variant 0.16
rpoA 3878391 c.117T>C synonymous_variant 0.17
rpoA 3878396 c.112C>T synonymous_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 0.93
clpC1 4038368 c.2337T>C synonymous_variant 0.15
clpC1 4038388 c.2317T>C synonymous_variant 0.14
clpC1 4038398 c.2307G>T synonymous_variant 0.13
clpC1 4038434 c.2271G>C synonymous_variant 0.13
clpC1 4038444 p.Ala754Lys missense_variant 0.13
clpC1 4038498 p.Ser736Thr missense_variant 0.16
clpC1 4038530 p.Glu725Asp missense_variant 0.16
clpC1 4038536 c.2169C>T synonymous_variant 0.15
clpC1 4038596 c.2109A>G synonymous_variant 0.16
clpC1 4038623 c.2082A>G synonymous_variant 0.16
clpC1 4038640 p.Asp689Asn missense_variant 0.16
clpC1 4038653 c.2052C>T synonymous_variant 0.14
clpC1 4038658 p.Lys683Gln missense_variant 0.13
clpC1 4038661 p.Ser682Thr missense_variant 0.13
clpC1 4038662 c.2043T>C synonymous_variant 0.13
clpC1 4038671 c.2034T>C synonymous_variant 0.13
clpC1 4038683 c.2022T>C synonymous_variant 0.15
clpC1 4038695 c.2010C>G synonymous_variant 0.16
clpC1 4038701 c.2004G>C synonymous_variant 0.14
clpC1 4038704 c.2001T>C synonymous_variant 0.15
clpC1 4038707 c.1998C>G synonymous_variant 0.15
clpC1 4038710 c.1995G>C synonymous_variant 0.15
clpC1 4038713 c.1992T>C synonymous_variant 0.15
clpC1 4038740 c.1965G>C synonymous_variant 0.15
clpC1 4038755 c.1950G>C synonymous_variant 0.15
clpC1 4038773 c.1932T>C synonymous_variant 0.17
clpC1 4038782 c.1923G>C synonymous_variant 0.18
clpC1 4038790 c.1915C>T synonymous_variant 0.15
clpC1 4038812 c.1893T>C synonymous_variant 0.16
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 0.21
clpC1 4038908 c.1797C>G synonymous_variant 0.2
clpC1 4038914 c.1791G>C synonymous_variant 0.2
clpC1 4038923 c.1782A>G synonymous_variant 0.19
clpC1 4038932 c.1773G>C synonymous_variant 0.21
clpC1 4038953 c.1752A>G synonymous_variant 0.21
clpC1 4038956 c.1749T>C synonymous_variant 0.23
clpC1 4038965 c.1740T>C synonymous_variant 0.25
clpC1 4038971 c.1734T>C synonymous_variant 0.26
clpC1 4038974 c.1731T>C synonymous_variant 0.23
clpC1 4038989 c.1716T>C synonymous_variant 0.22
clpC1 4038997 c.1708T>C synonymous_variant 0.23
clpC1 4039022 c.1683A>G synonymous_variant 0.21
clpC1 4039073 c.1632C>G synonymous_variant 0.19
clpC1 4039085 c.1620A>G synonymous_variant 0.17
clpC1 4039090 c.1615C>T synonymous_variant 0.19
clpC1 4039097 c.1608G>C synonymous_variant 0.19
clpC1 4039103 c.1602T>C synonymous_variant 0.17
clpC1 4039106 c.1599G>C synonymous_variant 0.16
clpC1 4039112 c.1593C>G synonymous_variant 0.15
clpC1 4039121 c.1584T>C synonymous_variant 0.16
clpC1 4039124 c.1581C>G synonymous_variant 0.17
clpC1 4039127 c.1578G>A synonymous_variant 0.17
clpC1 4039142 c.1563A>G synonymous_variant 0.17
clpC1 4039145 c.1560G>C synonymous_variant 0.16
clpC1 4039169 p.Glu512Asp missense_variant 0.15
clpC1 4039183 c.1522T>C synonymous_variant 0.13
clpC1 4039268 c.1437C>G synonymous_variant 0.15
clpC1 4039274 c.1431G>C synonymous_variant 0.15
clpC1 4039286 c.1419T>C synonymous_variant 0.14
clpC1 4039289 c.1416T>C synonymous_variant 0.14
clpC1 4039295 c.1410A>C synonymous_variant 0.14
clpC1 4039298 c.1407T>C synonymous_variant 0.15
clpC1 4039319 c.1386T>C synonymous_variant 0.18
clpC1 4039322 c.1383T>C synonymous_variant 0.18
clpC1 4039328 c.1377A>T synonymous_variant 0.18
clpC1 4039334 c.1371G>C synonymous_variant 0.16
clpC1 4039337 p.Thr456Gln missense_variant 0.16
clpC1 4039364 c.1341C>G synonymous_variant 0.17
clpC1 4039388 c.1317C>A synonymous_variant 0.17
clpC1 4039391 c.1314T>G synonymous_variant 0.16
clpC1 4039409 c.1296T>C synonymous_variant 0.13
clpC1 4039412 c.1293T>G synonymous_variant 0.13
clpC1 4039789 p.Ser306Thr missense_variant 0.13
embC 4241264 p.Gly468Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0