TB-Profiler result

Run: SRR13861202
Summary

Run ID: SRR13861202

Sample name:

Date: 03-04-2023 09:25:54

Number of reads: 640121

Percentage reads mapped: 16.02

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 0.25 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 6667 p.Gln476His missense_variant 1.0
gyrA 7289 c.-13_-12insT upstream_gene_variant 1.0
rpoB 760214 p.Asn136Lys missense_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.24
rpoB 761129 c.1323G>C synonymous_variant 0.25
rpoB 761133 p.Leu443Ile missense_variant 0.24
rpoB 761150 c.1344A>C synonymous_variant 0.21
rpoB 761151 p.Leu449Val missense_variant 0.21
rpoB 761156 c.1350G>C synonymous_variant 0.2
rpoB 761162 c.1356G>C synonymous_variant 0.2
rpoB 761165 c.1359G>C synonymous_variant 0.2
rpoB 761168 c.1362C>G synonymous_variant 0.2
rpoB 761178 p.Ser458Thr missense_variant 0.19
rpoB 761192 c.1386C>G synonymous_variant 0.19
rpoB 761195 c.1389G>C synonymous_variant 0.19
rpoB 761196 p.Leu464Phe missense_variant 0.2
rpoB 761204 c.1398C>T synonymous_variant 0.22
rpoB 761207 c.1401C>T synonymous_variant 0.22
rpoB 761213 c.1407G>A synonymous_variant 0.21
rpoB 761220 p.Ser472Thr missense_variant 0.19
rpoB 761234 c.1428G>C synonymous_variant 0.19
rpoB 761235 p.Met477Val missense_variant 0.19
rpoC 764446 c.1077T>C synonymous_variant 0.13
rpoC 764451 p.Gly361Ala missense_variant 0.13
rpoC 764470 c.1101C>G synonymous_variant 0.11
rpoC 764471 p.Asn368Arg missense_variant 0.11
rpoC 764485 c.1116G>C synonymous_variant 0.11
rpoC 764498 p.Ser377Ala missense_variant 0.11
rpoC 764503 c.1134G>C synonymous_variant 0.11
rpoC 764509 c.1140G>C synonymous_variant 0.11
rpoC 764521 c.1152T>C synonymous_variant 0.11
fbiC 1304005 p.Pro359Ser missense_variant 1.0
rrs 1471943 n.98T>C non_coding_transcript_exon_variant 1.0
rrs 1472075 n.230A>C non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>T non_coding_transcript_exon_variant 1.0
rrs 1473370 n.1525T>C non_coding_transcript_exon_variant 1.0
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.6
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.64
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.64
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.65
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.66
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.69
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.69
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.69
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.69
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.69
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.72
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.71
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.72
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.72
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.74
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.72
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.69
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.69
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.67
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.36
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.23
fabG1 1673813 p.Arg125Leu missense_variant 1.0
inhA 1674784 p.Arg195Gly missense_variant 1.0
ndh 2101793 p.Trp417* stop_gained 0.93
PPE35 2169624 p.Gly330Asp missense_variant 1.0
kasA 2519223 p.Thr370Ile missense_variant 1.0
ahpC 2726213 c.21C>T synonymous_variant 1.0
ribD 2987016 p.Gly60Arg missense_variant 1.0
Rv2752c 3065644 p.Thr183Ser missense_variant 1.0
thyA 3074595 c.-124C>A upstream_gene_variant 1.0
alr 3841581 c.-161T>A upstream_gene_variant 1.0
embC 4242810 p.Leu983Gln missense_variant 1.0
embB 4246553 p.Arg14Trp missense_variant 1.0
embB 4248920 p.Val803Met missense_variant 1.0
embB 4249551 p.Arg1013Leu missense_variant 1.0
ethA 4326296 p.Leu393Gln missense_variant 1.0