TB-Profiler result

Run: SRR13861565
Summary

Run ID: SRR13861565

Sample name:

Date: 03-04-2023 09:35:03

Number of reads: 621444

Percentage reads mapped: 15.55

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 0.19 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
gyrA 6715 c.-587C>T upstream_gene_variant 1.0
mshA 575693 p.Pro116Ala missense_variant 1.0
rpoB 759863 p.Gln19His missense_variant 1.0
rpoB 760399 p.Val198Ala missense_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.19
rpoB 761129 c.1323G>C synonymous_variant 0.18
rpoB 761133 p.Leu443Ile missense_variant 0.19
rpoB 761150 c.1344A>C synonymous_variant 0.2
rpoB 761151 p.Leu449Val missense_variant 0.2
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 0.24
rpoB 761168 c.1362C>G synonymous_variant 0.24
rpoB 761178 p.Ser458Thr missense_variant 0.24
rpoB 761192 c.1386C>G synonymous_variant 0.18
rpoB 761195 c.1389G>C synonymous_variant 0.22
rpoB 761196 p.Leu464Phe missense_variant 0.22
rpoB 761204 c.1398C>T synonymous_variant 0.24
rpoB 761207 c.1401C>T synonymous_variant 0.24
rpoB 761213 c.1407G>A synonymous_variant 0.19
rpoB 761220 p.Ser472Thr missense_variant 0.19
rpoB 761234 c.1428G>C synonymous_variant 0.16
rpoB 761235 p.Met477Val missense_variant 0.16
rpoB 763150 p.Phe1115Tyr missense_variant 1.0
rpoC 764516 p.Asp383Asn missense_variant 0.9
rpoC 766103 p.Arg912Gly missense_variant 1.0
mmpL5 777066 p.Ile472Ser missense_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.16
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.15
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.16
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.16
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.16
rrs 1472133 n.288G>A non_coding_transcript_exon_variant 0.16
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.16
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.16
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.17
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.17
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.16
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.16
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.17
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.17
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.18
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.18
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.18
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.13
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.12
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.13
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.13
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.13
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.12
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.12
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.14
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.12
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.12
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.12
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.13
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.66
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.78
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.77
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.78
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.76
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.79
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.77
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.78
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.78
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.78
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.79
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.79
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.82
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.81
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.8
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.79
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.78
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.77
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.75
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.75
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.38
ndh 2103185 c.-143A>C upstream_gene_variant 1.0
PPE35 2168894 c.1718dupG frameshift_variant 1.0
PPE35 2170039 p.Ala192Thr missense_variant 1.0
Rv1979c 2221777 p.Ala463Val missense_variant 1.0
kasA 2518793 p.Ser227Thr missense_variant 1.0
ahpC 2726300 c.108C>A synonymous_variant 1.0
folC 2747094 p.Asp169His missense_variant 1.0
Rv2752c 3064936 p.Ser419* stop_gained 1.0
Rv2752c 3065523 c.669C>T synonymous_variant 1.0
Rv2752c 3066039 c.153C>T synonymous_variant 1.0
alr 3841286 c.135T>A synonymous_variant 1.0
clpC1 4039368 p.Lys446Thr missense_variant 1.0
embC 4241777 p.Gly639Ser missense_variant 1.0
ubiA 4269888 c.-55C>A upstream_gene_variant 1.0