TB-Profiler result

Run: SRR6896383
Summary

Run ID: SRR6896383

Sample name:

Date: 04-04-2023 18:04:17

Number of reads: 496440

Percentage reads mapped: 93.58

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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 761127 p.Ser441Ala missense_variant 0.14 rifampicin
rpoB 761196 p.Leu464Met missense_variant 0.14 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
gyrB 6905 p.Ile556Val missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620653 c.767delG frameshift_variant 0.12
rpoB 761088 c.1282_1284delAGCinsTCG synonymous_variant 0.19
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 0.21
rpoB 761102 c.1296A>G synonymous_variant 0.23
rpoB 761132 c.1326G>C synonymous_variant 0.14
rpoB 761133 c.1327T>C synonymous_variant 0.14
rpoB 761138 c.1332C>G synonymous_variant 0.13
rpoB 761147 c.1341C>T synonymous_variant 0.13
rpoB 761150 c.1344A>C synonymous_variant 0.13
rpoB 761156 c.1350G>C synonymous_variant 0.13
rpoB 761162 c.1356G>C synonymous_variant 0.12
rpoB 761165 c.1359G>C synonymous_variant 0.12
rpoB 761168 c.1362C>G synonymous_variant 0.12
rpoB 761174 c.1368T>C synonymous_variant 0.11
rpoB 761180 c.1374A>C synonymous_variant 0.12
rpoB 761183 c.1377T>C synonymous_variant 0.13
rpoB 761186 p.Glu460Asp missense_variant 0.12
rpoB 761195 c.1389G>C synonymous_variant 0.14
rpoB 761207 c.1401C>T synonymous_variant 0.13
rpoB 762601 p.Trp932Leu missense_variant 0.11
rpoC 763622 p.Ala85Ser missense_variant 0.11
rpoC 763633 c.264T>C synonymous_variant 0.12
rpoC 763636 c.267T>C synonymous_variant 0.12
rpoC 763639 p.Glu90Asp missense_variant 0.12
rpoC 763642 c.273G>C synonymous_variant 0.12
rpoC 763660 c.291T>G synonymous_variant 0.12
rpoC 764311 c.942C>G synonymous_variant 0.11
rpoC 764371 c.1002G>C synonymous_variant 0.11
rpoC 764377 c.1008C>G synonymous_variant 0.1
rpoC 764521 c.1152T>C synonymous_variant 0.15
rpoC 764539 c.1170C>G synonymous_variant 0.17
rpoC 764542 c.1173C>G synonymous_variant 0.21
rpoC 764548 c.1179G>C synonymous_variant 0.19
rpoC 764560 c.1191T>C synonymous_variant 0.19
rpoC 764575 c.1206T>C synonymous_variant 0.21
rpoC 764581 c.1212T>C synonymous_variant 0.22
rpoC 764582 p.Leu405Met missense_variant 0.22
rpoC 764605 c.1236G>C synonymous_variant 0.23
rpoC 764611 c.1242G>T synonymous_variant 0.23
rpoC 764632 c.1263T>C synonymous_variant 0.25
rpoC 764635 c.1266C>G synonymous_variant 0.27
rpoC 764650 c.1281G>C synonymous_variant 0.32
rpoC 764665 c.1296C>G synonymous_variant 0.33
rpoC 764668 c.1299C>T synonymous_variant 0.29
rpoC 764671 c.1302G>C synonymous_variant 0.29
rpoC 764695 c.1326T>C synonymous_variant 0.2
rpoC 764706 p.Leu446Gln missense_variant 0.18
rpoC 764746 c.1377G>T synonymous_variant 0.15
rpoC 764749 c.1380G>C synonymous_variant 0.21
rpoC 764758 c.1389C>G synonymous_variant 0.21
rpoC 764764 c.1395T>C synonymous_variant 0.21
rpoC 764780 c.1411_1412delAGinsTC synonymous_variant 0.16
rpoC 764804 p.Gln479Phe missense_variant 0.15
rpoC 764809 c.1440C>T synonymous_variant 0.15
rpoC 764812 c.1443C>G synonymous_variant 0.15
rpoC 764815 c.1446A>G synonymous_variant 0.14
rpoC 764818 c.1449G>C synonymous_variant 0.15
rpoC 764824 c.1455T>C synonymous_variant 0.15
rpoC 764833 c.1464A>G synonymous_variant 0.16
rpoC 764843 p.Ala492Thr missense_variant 0.17
rpoC 764857 c.1488G>C synonymous_variant 0.2
rpoC 764858 c.1489T>C synonymous_variant 0.19
rpoC 764872 c.1503A>C synonymous_variant 0.19
rpoC 766174 p.Asn935Lys missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776222 c.2258dupG frameshift_variant 0.17
mmpL5 777416 c.1065G>T synonymous_variant 0.9
mmpR5 779357 p.Arg123Met missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800866 p.Ser20Gly missense_variant 0.1
fbiC 1303807 p.Gln293Lys missense_variant 0.14
fbiC 1304159 p.Val410Gly missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.11
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.15
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.16
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.15
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.14
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.14
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.21
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.21
rrs 1473022 n.1177G>A non_coding_transcript_exon_variant 0.16
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.16
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.1
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.11
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.11
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.11
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.1
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.22
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.2
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.2
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.2
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.11
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.11
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.13
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.13
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.13
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.12
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.12
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.12
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.16
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.14
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102596 c.447C>A synonymous_variant 0.11
ndh 2102807 p.Gln79Pro missense_variant 0.11
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170183 p.Trp144Arg missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715186 c.146delG frameshift_variant 0.1
folC 2746543 c.1056C>T synonymous_variant 0.11
thyX 3067643 p.Tyr101* stop_gained 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.29
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448954 p.Pro151Thr missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612117 p.Gly334Arg missense_variant 0.25
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
clpC1 4039865 c.840T>G synonymous_variant 0.11
clpC1 4039871 c.834C>G synonymous_variant 0.11
clpC1 4039875 p.Asn277Arg missense_variant 0.12
clpC1 4039898 c.807C>G synonymous_variant 0.2
clpC1 4039904 c.801A>G synonymous_variant 0.21
clpC1 4039916 c.789T>C synonymous_variant 0.23
clpC1 4039922 c.783C>T synonymous_variant 0.2
clpC1 4039929 c.775_776delAGinsTC synonymous_variant 0.17
clpC1 4039931 c.774T>C synonymous_variant 0.17
clpC1 4039934 c.771G>C synonymous_variant 0.17
clpC1 4039940 c.765G>C synonymous_variant 0.17
clpC1 4039943 c.762G>C synonymous_variant 0.17
clpC1 4039946 c.759A>C synonymous_variant 0.17
clpC1 4039949 c.756G>C synonymous_variant 0.17
clpC1 4039952 c.753T>C synonymous_variant 0.17
clpC1 4039960 p.Thr249Ser missense_variant 0.18
clpC1 4039974 p.Asp244Gly missense_variant 0.18
clpC1 4039977 p.Lys243Arg missense_variant 0.18
clpC1 4039988 c.717C>G synonymous_variant 0.18
clpC1 4039991 c.714G>C synonymous_variant 0.18
clpC1 4039994 p.Glu237Asp missense_variant 0.18
clpC1 4040001 p.His235Arg missense_variant 0.17
clpC1 4040003 p.Val234Asp missense_variant 0.17
clpC1 4040009 c.696C>G synonymous_variant 0.17
clpC1 4040015 c.690G>C synonymous_variant 0.15
clpC1 4040021 c.684A>C synonymous_variant 0.15
clpC1 4040024 c.681A>G synonymous_variant 0.15
clpC1 4040033 c.672G>C synonymous_variant 0.16
clpC1 4040063 c.642G>C synonymous_variant 0.15
clpC1 4040069 c.636G>C synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245764 c.-750G>T upstream_gene_variant 0.2
embA 4246329 p.Thr1033Ala missense_variant 0.18
ubiA 4269511 p.Val108Gly missense_variant 0.43
aftB 4269590 c.-754C>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0