TB-Profiler result

Run: ERR11466174
Summary

Run ID: ERR11466174

Sample name:

Date: 08-01-2024 04:02:26

Number of reads: 2654665

Percentage reads mapped: 97.8

Strain: lineage4.8

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
Rifampicin
Isoniazid
Ethambutol R embB p.Asn399Asp (0.13)
Pyrazinamide
Streptomycin R rrs n.462C>T (0.15)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
embB 4247708 p.Asn399Asp missense_variant 0.13 ethambutol
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 0.99
ccsA 620265 c.375C>G synonymous_variant 0.15
ccsA 620268 c.378G>C synonymous_variant 0.14
ccsA 620283 c.393T>C synonymous_variant 0.13
ccsA 620284 p.Ala132Pro missense_variant 0.12
ccsA 620288 p.Arg133Gln missense_variant 0.12
ccsA 620295 c.405G>T synonymous_variant 0.13
ccsA 620298 c.408G>C synonymous_variant 0.13
ccsA 620310 c.420C>T synonymous_variant 0.15
ccsA 620317 p.Val143Leu missense_variant 0.14
ccsA 620733 c.843G>C synonymous_variant 0.12
ccsA 620734 c.844C>A synonymous_variant 0.12
ccsA 620739 c.849A>G synonymous_variant 0.12
ccsA 620742 c.852G>C synonymous_variant 0.12
ccsA 620745 c.855G>C synonymous_variant 0.12
ccsA 620748 c.858T>A synonymous_variant 0.12
ccsA 620763 c.873G>A synonymous_variant 0.15
ccsA 620769 c.879C>G synonymous_variant 0.14
rpoB 761150 c.1344A>C synonymous_variant 0.18
rpoB 761153 c.1347G>C synonymous_variant 0.16
rpoB 761165 c.1359G>C synonymous_variant 0.17
rpoB 761180 c.1374A>C synonymous_variant 0.18
rpoB 761189 c.1383T>C synonymous_variant 0.19
rpoB 761195 c.1389G>C synonymous_variant 0.19
rpoB 761207 c.1401C>T synonymous_variant 0.19
rpoB 761213 c.1407G>C synonymous_variant 0.18
rpoB 761219 c.1413G>C synonymous_variant 0.18
rpoB 761255 c.1449T>G synonymous_variant 0.13
rpoB 761261 c.1455G>T synonymous_variant 0.13
rpoB 762131 c.2325C>G synonymous_variant 0.14
rpoB 762206 c.2400C>G synonymous_variant 0.14
rpoB 762233 c.2427G>C synonymous_variant 0.14
rpoB 762246 c.2440C>T synonymous_variant 0.16
rpoB 762254 c.2448T>G synonymous_variant 0.17
rpoB 762257 c.2451C>G synonymous_variant 0.15
rpoB 762266 c.2460T>C synonymous_variant 0.13
rpoB 762284 c.2478G>C synonymous_variant 0.14
rpoB 762293 c.2487T>C synonymous_variant 0.14
rpoC 763028 c.-342T>C upstream_gene_variant 0.13
rpoC 763031 c.-339T>G upstream_gene_variant 0.14
rpoC 763034 c.-336C>G 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 763148 c.-222G>C upstream_gene_variant 0.15
rpoC 763158 c.-212C>T upstream_gene_variant 0.14
rpoC 763166 c.-204A>G upstream_gene_variant 0.15
rpoC 763190 c.-180C>T upstream_gene_variant 0.13
rpoC 764353 c.984G>C synonymous_variant 0.15
rpoC 764365 c.996C>T synonymous_variant 0.14
rpoC 764510 c.1141C>T synonymous_variant 0.13
rpoC 764521 c.1152T>C synonymous_variant 0.13
rpoC 764527 c.1158C>T synonymous_variant 0.13
rpoC 764536 c.1167G>C synonymous_variant 0.14
rpoC 764539 c.1170C>G synonymous_variant 0.17
rpoC 764548 c.1179G>A synonymous_variant 0.18
rpoC 764551 c.1182G>C synonymous_variant 0.17
rpoC 764554 c.1185C>T synonymous_variant 0.16
rpoC 764560 c.1191T>C synonymous_variant 0.17
rpoC 764566 c.1197C>G synonymous_variant 0.16
rpoC 764575 c.1206T>G synonymous_variant 0.17
rpoC 764593 c.1224C>T synonymous_variant 0.14
rpoC 764611 c.1242G>T synonymous_variant 0.15
rpoC 765883 c.2514C>G synonymous_variant 0.13
rpoC 765886 c.2517C>G synonymous_variant 0.13
rpoC 766462 c.3093G>C synonymous_variant 0.14
rpoC 766483 c.3114G>C synonymous_variant 0.16
rpoC 766484 p.Val1039Ile missense_variant 0.16
rpoC 766492 c.3123T>C synonymous_variant 0.17
rpoC 766522 c.3153C>G synonymous_variant 0.16
rpoC 766528 c.3159T>C synonymous_variant 0.15
rpoC 766531 c.3162G>C synonymous_variant 0.14
rpoC 766540 p.Asp1057Glu missense_variant 0.14
rpoC 766549 c.3180G>C synonymous_variant 0.17
rpoC 766765 c.3396A>C synonymous_variant 0.14
rpoC 766801 c.3432C>G synonymous_variant 0.15
rpoC 766804 c.3435A>G synonymous_variant 0.15
rpoC 766861 c.3492G>C synonymous_variant 0.16
rpoC 766864 c.3495G>C synonymous_variant 0.16
rpoC 766933 c.3564A>G synonymous_variant 0.15
rpoC 766945 c.3576A>G synonymous_variant 0.16
rpoC 766963 c.3594T>C synonymous_variant 0.14
rpoC 766972 c.3603G>C synonymous_variant 0.17
rpoC 766996 c.3627C>T synonymous_variant 0.15
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.15
rpoC 767014 c.3645G>C synonymous_variant 0.14
rpoC 767033 c.3664_3666delTCGinsAGC synonymous_variant 0.14
rpoC 767059 c.3690T>G synonymous_variant 0.19
rpoC 767062 c.3693C>A synonymous_variant 0.18
rpoC 767098 c.3729T>C synonymous_variant 0.15
rpoC 767119 c.3750A>G synonymous_variant 0.16
rpoC 767134 c.3765C>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800627 c.-182C>T upstream_gene_variant 0.13
rplC 800648 c.-161A>T upstream_gene_variant 0.13
fbiC 1304580 c.1650T>C synonymous_variant 0.15
fbiC 1304613 c.1683T>C synonymous_variant 0.18
fbiC 1304634 c.1704C>G synonymous_variant 0.16
fbiC 1304640 c.1710A>C synonymous_variant 0.15
fbiC 1304646 c.1716T>C synonymous_variant 0.15
fbiC 1304778 c.1848T>C synonymous_variant 0.15
fbiC 1304784 c.1854T>C synonymous_variant 0.14
fbiC 1304787 c.1857T>G synonymous_variant 0.14
fbiC 1304937 c.2007G>C synonymous_variant 0.21
fbiC 1304958 c.2028T>G synonymous_variant 0.21
fbiC 1304983 c.2053C>T synonymous_variant 0.21
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 0.15
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.14
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.17
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.14
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.14
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.15
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.15
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.15
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.13
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.15
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.13
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.13
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.14
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.15
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.15
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.17
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.13
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 1475642 n.1985T>C non_coding_transcript_exon_variant 0.12
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.18
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.18
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.21
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15
rpsA 1833589 c.48A>T synonymous_variant 0.16
rpsA 1833595 c.54T>C synonymous_variant 0.16
rpsA 1833661 c.120A>G synonymous_variant 0.15
rpsA 1833667 c.126C>G synonymous_variant 0.14
rpsA 1833940 c.399C>G synonymous_variant 0.13
rpsA 1833971 c.430C>T synonymous_variant 0.14
rpsA 1833979 c.438T>C synonymous_variant 0.15
rpsA 1834000 c.459G>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 0.98
PPE35 2168149 p.Pro822Ser missense_variant 0.96
PPE35 2169149 c.1464G>C synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.13
rpoA 3877613 p.Ile299Val missense_variant 0.12
rpoA 3877656 c.852T>G synonymous_variant 0.14
rpoA 3878298 c.210A>G synonymous_variant 0.13
rpoA 3878304 c.204G>C synonymous_variant 0.14
rpoA 3878313 c.195G>C synonymous_variant 0.14
rpoA 3878322 c.186A>G synonymous_variant 0.16
rpoA 3878331 c.177A>G synonymous_variant 0.19
rpoA 3878334 c.174T>C synonymous_variant 0.18
rpoA 3878337 c.171T>C synonymous_variant 0.18
rpoA 3878346 c.162T>C synonymous_variant 0.21
rpoA 3878364 c.144A>T synonymous_variant 0.19
rpoA 3878367 c.141C>G synonymous_variant 0.21
rpoA 3878376 c.132G>C synonymous_variant 0.19
rpoA 3878385 c.123C>G synonymous_variant 0.19
rpoA 3878388 c.120C>G synonymous_variant 0.18
rpoA 3878391 c.117T>C synonymous_variant 0.19
rpoA 3878415 c.93C>T synonymous_variant 0.17
rpoA 3878424 c.84G>C synonymous_variant 0.16
rpoA 3878436 c.72A>G synonymous_variant 0.16
rpoA 3878442 c.66G>C synonymous_variant 0.15
rpoA 3878454 c.54A>C synonymous_variant 0.16
clpC1 4038749 c.1956C>G synonymous_variant 0.14
clpC1 4038755 c.1950G>T synonymous_variant 0.15
clpC1 4038770 c.1935C>T synonymous_variant 0.15
clpC1 4038773 c.1932T>C synonymous_variant 0.15
clpC1 4038782 c.1923G>C synonymous_variant 0.16
clpC1 4038812 c.1893T>C synonymous_variant 0.12
clpC1 4038845 c.1860G>C synonymous_variant 0.13
clpC1 4038860 c.1845G>C synonymous_variant 0.13
clpC1 4038878 c.1827A>G synonymous_variant 0.13
clpC1 4038914 c.1791G>C synonymous_variant 0.13
clpC1 4038953 c.1752A>G synonymous_variant 0.13
clpC1 4038956 c.1749T>C synonymous_variant 0.13
clpC1 4038965 c.1740T>C synonymous_variant 0.13
clpC1 4038989 c.1716T>C synonymous_variant 0.2
clpC1 4038997 c.1708T>C synonymous_variant 0.18
clpC1 4039004 c.1701C>G synonymous_variant 0.18
clpC1 4039022 c.1683A>G synonymous_variant 0.24
clpC1 4039064 c.1641C>T synonymous_variant 0.18
clpC1 4039097 c.1608G>C synonymous_variant 0.12
clpC1 4039517 c.1188C>G synonymous_variant 0.14
clpC1 4039729 p.Asp326Asn missense_variant 0.94
clpC1 4039898 c.807C>G synonymous_variant 0.13
clpC1 4040318 c.387C>G synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246305 p.Ser1025Glu missense_variant 0.14
embA 4246308 p.Thr1026Ala missense_variant 0.14
embB 4246316 c.-198T>G upstream_gene_variant 0.13
embB 4246319 c.-195G>C upstream_gene_variant 0.12
embB 4247491 c.978G>C synonymous_variant 0.13
embB 4247539 c.1026T>C synonymous_variant 0.14
embB 4247746 c.1233C>T synonymous_variant 0.12
embB 4247761 c.1248T>C synonymous_variant 0.13
embB 4247773 c.1260G>A synonymous_variant 0.13
embB 4247776 c.1263G>T synonymous_variant 0.14
embB 4247797 c.1284C>G synonymous_variant 0.15
embB 4247800 c.1287A>T synonymous_variant 0.16
embB 4247803 c.1290G>C synonymous_variant 0.17
embB 4247815 c.1302C>G synonymous_variant 0.14
embB 4247819 p.Val436Ile missense_variant 0.16
embB 4247830 c.1317A>G synonymous_variant 0.13
embB 4247866 c.1353G>C synonymous_variant 0.15
embB 4247875 c.1362G>C synonymous_variant 0.15
embB 4247876 c.1363C>T synonymous_variant 0.15
embB 4247881 c.1368G>C synonymous_variant 0.15
embB 4247887 c.1374C>T synonymous_variant 0.14
embB 4247905 c.1392G>C synonymous_variant 0.12
embB 4247956 c.1443G>C synonymous_variant 0.16
embB 4247974 c.1461C>G synonymous_variant 0.15
embB 4248007 c.1494C>G synonymous_variant 0.13
embB 4248035 p.Val508Ile missense_variant 0.14
embB 4248040 c.1527C>G synonymous_variant 0.13
embB 4248041 p.Ala510Thr missense_variant 0.13
embB 4248044 p.Lys511Ala missense_variant 0.14
embB 4248070 c.1557T>C synonymous_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0