TB-Profiler result

Run: SRR13861560
Summary

Run ID: SRR13861560

Sample name:

Date: 03-04-2023 09:34:55

Number of reads: 586893

Percentage reads mapped: 14.69

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 761131 p.Gly442Glu missense_variant 0.23 rifampicin
ethA 4326568 c.905delT frameshift_variant 1.0 ethionamide
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 8820 p.Asp507His missense_variant 1.0
mshA 575967 p.Val207Asp missense_variant 1.0
rpoB 759961 p.Thr52Asn missense_variant 1.0
rpoB 761102 c.1296A>G synonymous_variant 0.11
rpoB 761126 c.1320G>T synonymous_variant 0.23
rpoB 761129 c.1323G>C synonymous_variant 0.23
rpoB 761133 p.Leu443Ile missense_variant 0.22
rpoB 761150 c.1344A>C synonymous_variant 0.23
rpoB 761151 p.Leu449Val missense_variant 0.22
rpoB 761156 c.1350G>C synonymous_variant 0.22
rpoB 761162 c.1356G>C synonymous_variant 0.22
rpoB 761165 c.1359G>C synonymous_variant 0.23
rpoB 761168 c.1362C>G synonymous_variant 0.23
rpoB 761178 p.Ser458Thr missense_variant 0.22
rpoB 761192 c.1386C>G synonymous_variant 0.23
rpoB 761195 c.1389G>C synonymous_variant 0.23
rpoB 761196 p.Leu464Phe missense_variant 0.23
rpoB 761204 c.1398C>T synonymous_variant 0.18
rpoB 761207 c.1401C>T synonymous_variant 0.21
rpoB 761213 c.1407G>A synonymous_variant 0.22
rpoB 761220 p.Ser472Thr missense_variant 0.21
rpoB 761234 c.1428G>C synonymous_variant 0.19
rpoB 761235 p.Met477Val missense_variant 0.19
rpoB 763050 p.Leu1082Met missense_variant 1.0
rpoC 764470 c.1101C>G synonymous_variant 0.12
rpoC 764471 p.Asn368Arg missense_variant 0.12
rpoC 764479 c.1110G>A synonymous_variant 0.12
rpoC 764485 c.1116G>C synonymous_variant 0.13
rpoC 764498 p.Ser377Ala missense_variant 0.14
rpoC 764503 c.1134G>C synonymous_variant 0.14
rpoC 764509 c.1140G>C synonymous_variant 0.15
rpoC 764513 p.Phe382Leu missense_variant 0.14
rpoC 764521 c.1152T>C synonymous_variant 0.17
mmpL5 775701 p.Pro927Gln missense_variant 1.0
mmpL5 778828 c.-348G>A upstream_gene_variant 1.0
rplC 801353 p.Val182Ala missense_variant 1.0
fbiC 1304512 p.Val528Ile missense_variant 1.0
embR 1417485 c.-138T>G upstream_gene_variant 0.2
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.4
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.46
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.44
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.43
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.43
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.43
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.41
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.44
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.44
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.41
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.44
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.41
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.46
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.46
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.48
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.5
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.48
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.29
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.3
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.15
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.6
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.67
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.65
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.67
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.68
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.72
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.7
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.71
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.71
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.71
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.73
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.73
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.72
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.73
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.72
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.73
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.69
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.7
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.67
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.68
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.45
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.17
rpsA 1834175 p.Arg212* stop_gained 1.0
Rv1979c 2222085 c.1080G>C synonymous_variant 1.0
folC 2746135 c.1464A>C stop_lost&splice_region_variant 1.0
ald 3087218 p.Met133Ile missense_variant 1.0
whiB7 3568679 p.Val1Leu missense_variant 1.0
clpC1 4040066 c.639G>T synonymous_variant 1.0
embC 4241259 c.1397_1398insT frameshift_variant 1.0
embA 4243358 c.126C>T synonymous_variant 1.0
embA 4243469 c.237C>T synonymous_variant 1.0
embB 4248436 c.1923C>T synonymous_variant 1.0
ubiA 4269557 p.Ala93Pro missense_variant 1.0