TB-Profiler result

Run: ERR4820394
Summary

Run ID: ERR4820394

Sample name:

Date: 01-04-2023 16:39:37

Number of reads: 806496

Percentage reads mapped: 44.8

Strain: lineage4.3.4.2.1

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 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
tlyA 1917946 p.Arg3* stop_gained 0.1 capreomycin
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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575930 p.Glu195Lys missense_variant 0.17
rpoB 760907 p.Phe367Leu missense_variant 0.12
rpoB 762185 c.2379G>C synonymous_variant 0.12
rpoB 762206 c.2400C>G synonymous_variant 0.13
rpoB 762209 c.2403C>G synonymous_variant 0.13
rpoB 762218 c.2412T>C synonymous_variant 0.14
rpoB 762243 p.Arg813Lys missense_variant 0.12
rpoB 762251 c.2445G>C synonymous_variant 0.12
rpoB 762254 c.2448T>C synonymous_variant 0.12
rpoB 762266 c.2460T>C synonymous_variant 0.1
rpoC 762863 c.-507T>C upstream_gene_variant 0.14
rpoB 762872 p.Met1022Ile missense_variant 0.21
rpoB 762878 p.Ile1024Met missense_variant 0.23
rpoB 762879 p.Met1025Leu missense_variant 0.24
rpoC 762894 c.-476C>T upstream_gene_variant 0.2
rpoC 762920 c.-450C>T upstream_gene_variant 0.19
rpoB 762925 p.Thr1040Ile missense_variant 0.18
rpoC 762929 c.-441G>C upstream_gene_variant 0.19
rpoC 762932 c.-438G>C upstream_gene_variant 0.19
rpoB 762939 p.Met1045Leu missense_variant 0.19
rpoB 762942 p.Ile1046Val missense_variant 0.19
rpoC 762962 c.-408C>T upstream_gene_variant 0.18
rpoC 762965 c.-405T>C upstream_gene_variant 0.17
rpoC 762980 c.-390T>C upstream_gene_variant 0.19
rpoC 762989 c.-381G>C upstream_gene_variant 0.19
rpoC 762995 c.-375G>C upstream_gene_variant 0.2
rpoC 764070 p.Leu234Pro missense_variant 0.13
rpoC 764377 c.1008C>G synonymous_variant 0.12
rpoC 764380 c.1011G>C synonymous_variant 0.13
rpoC 764387 c.1018T>C synonymous_variant 0.2
rpoC 764392 c.1023C>T synonymous_variant 0.19
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.19
rpoC 764410 c.1041G>C synonymous_variant 0.17
rpoC 764428 c.1059G>C synonymous_variant 0.14
rpoC 764434 c.1065A>G synonymous_variant 0.14
rpoC 764435 c.1066A>C synonymous_variant 0.14
rpoC 764446 p.Asp359Glu missense_variant 0.17
rpoC 764450 p.Gly361Arg missense_variant 0.16
rpoC 764455 c.1086G>C synonymous_variant 0.17
rpoC 764458 c.1089G>C synonymous_variant 0.17
rpoC 764461 p.Glu364Asp missense_variant 0.17
rpoC 764470 c.1101C>G synonymous_variant 0.17
rpoC 764471 p.Asn368Arg missense_variant 0.17
rpoC 764485 c.1116G>C synonymous_variant 0.36
rpoC 764497 c.1128A>G synonymous_variant 0.38
rpoC 764498 p.Ser377Ala missense_variant 0.38
rpoC 764521 c.1152T>C synonymous_variant 0.32
rpoC 764527 c.1158C>G synonymous_variant 0.28
rpoC 764533 c.1164C>G synonymous_variant 0.29
rpoC 764537 p.Pro390Ala missense_variant 0.29
rpoC 764540 p.Val391Ile missense_variant 0.29
rpoC 764543 c.1176delC frameshift_variant 0.29
rpoC 764549 c.1181_1182delCG frameshift_variant 0.29
rpoC 764553 p.Gly395Ala missense_variant 0.29
rpoC 764557 c.1188_1189insAAG conservative_inframe_insertion 0.31
rpoC 764560 c.1191T>G synonymous_variant 0.31
rpoC 764566 c.1197C>G synonymous_variant 0.41
rpoC 764575 c.1206T>C synonymous_variant 0.53
rpoC 764581 c.1212T>C synonymous_variant 0.53
rpoC 764582 p.Leu405Met missense_variant 0.53
rpoC 764587 c.1218C>G synonymous_variant 0.53
rpoC 764623 c.1254C>G synonymous_variant 0.38
rpoC 764632 c.1263T>C synonymous_variant 0.29
rpoC 764641 c.1272C>T synonymous_variant 0.29
rpoC 764644 c.1275G>C synonymous_variant 0.27
rpoC 764650 c.1281G>T synonymous_variant 0.25
rpoC 764656 c.1287C>G synonymous_variant 0.25
rpoC 764665 c.1296C>G synonymous_variant 0.24
rpoC 764668 c.1299C>T synonymous_variant 0.22
rpoC 764671 c.1302G>C synonymous_variant 0.21
rpoC 764672 p.Gln435Glu missense_variant 0.21
rpoC 764677 c.1308C>G synonymous_variant 0.2
rpoC 764695 c.1326T>C synonymous_variant 0.17
rpoC 764701 c.1332C>G synonymous_variant 0.17
rpoC 764705 p.Leu446Lys missense_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766441 c.3072C>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776169 p.Gly771Val missense_variant 0.18
mmpL5 779280 c.-800G>A upstream_gene_variant 0.11
mmpS5 779596 c.-693_-692dupAC upstream_gene_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.6
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.6
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.6
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.6
rrs 1472970 n.1125C>T non_coding_transcript_exon_variant 0.6
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.6
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.6
rrs 1472975 n.1130T>G non_coding_transcript_exon_variant 0.6
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.6
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.6
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.6
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.6
rrs 1472993 n.1148G>A non_coding_transcript_exon_variant 0.6
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.6
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.6
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.6
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.6
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.75
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.75
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.67
fabG1 1674176 p.Gly246Asp missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074648 c.-177T>G upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3641083 p.Pro181Ser missense_variant 0.12
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.89
clpC1 4039996 p.Glu237Lys missense_variant 0.12
panD 4043938 p.Ile115Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268278 p.Pro187Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408192 p.Ile4Asn missense_variant 0.12