TB-Profiler result

Run: SRR13861255
Summary

Run ID: SRR13861255

Sample name:

Date: 03-04-2023 09:27:16

Number of reads: 453194

Percentage reads mapped: 22.68

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 0.14 rifampicin
rpoB 761135 p.Leu443Phe missense_variant 0.15 rifampicin
embC 4240748 p.Tyr296His missense_variant 1.0 ethambutol
embB 4247959 p.Met482Ile missense_variant 1.0 ethambutol
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
fgd1 491360 p.Ile193Ser missense_variant 1.0
mshA 576396 p.Ser350Ile missense_variant 1.0
rpoB 760225 p.Glu140Ala missense_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.14
rpoB 761129 c.1323G>C synonymous_variant 0.14
rpoB 761150 c.1344A>C synonymous_variant 0.14
rpoB 761151 p.Leu449Val missense_variant 0.14
rpoB 761156 c.1350G>C synonymous_variant 0.12
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 761178 p.Ser458Thr missense_variant 0.11
rpoB 761196 p.Leu464Phe missense_variant 0.12
rpoB 761204 c.1398C>T synonymous_variant 0.12
rpoB 761213 c.1407G>A synonymous_variant 0.12
rpoB 761220 p.Ser472Thr missense_variant 0.11
rpoB 761235 p.Met477Val missense_variant 0.11
rpoC 767186 p.Gln1273* stop_gained 0.93
mmpR5 779067 p.Tyr26* stop_gained 1.0
rplC 800933 p.Pro42His missense_variant 1.0
fbiC 1305306 c.2376A>T synonymous_variant 1.0
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.11
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.12
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.12
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.12
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.12
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.11
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.11
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.42
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.58
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.58
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.58
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.6
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.64
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.64
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.64
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.64
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.64
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.62
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.62
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.63
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.63
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.62
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.6
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.6
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.6
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.63
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.64
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.3
tlyA 1918560 c.621G>T synonymous_variant 1.0
ndh 2102402 p.Leu214Arg missense_variant 1.0
katG 2156175 c.-64T>G upstream_gene_variant 1.0
PPE35 2169349 p.Phe422Ile missense_variant 1.0
PPE35 2170540 p.Leu25Val missense_variant 1.0
pncA 2288999 p.Phe81Leu missense_variant 1.0
fbiD 3339660 c.543C>G synonymous_variant 1.0
Rv3236c 3612627 p.Ala164Thr missense_variant 1.0
embA 4244119 p.Tyr296Phe missense_variant 1.0
embB 4247417 p.Tyr302Asn missense_variant 1.0
embB 4248036 p.Val508Gly missense_variant 1.0
embB 4248325 c.1812G>C synonymous_variant 1.0
aftB 4267246 p.Asn531His missense_variant 0.18
aftB 4267894 p.Ile315Phe missense_variant 1.0
ethA 4326052 p.Asp474Glu missense_variant 1.0
ethA 4327388 p.Thr29Ile missense_variant 0.95
ethR 4328162 p.His205Pro missense_variant 1.0
whiB6 4338518 c.4C>A synonymous_variant 1.0