TB-Profiler result

Run: SRR5818446
Summary

Run ID: SRR5818446

Sample name:

Date: 04-04-2023 11:30:06

Number of reads: 890191

Percentage reads mapped: 98.57

Strain: lineage4.9

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
lineage4.9 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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.22 streptomycin
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 6454 c.-848C>T upstream_gene_variant 0.98
gyrA 6721 c.-581C>T upstream_gene_variant 0.97
gyrA 7585 p.Ser95Thr missense_variant 1.0
mmpL5 779283 c.-803G>A upstream_gene_variant 0.97
mmpL5 779295 c.-815A>G upstream_gene_variant 0.97
mmpR5 779431 p.Asn148Gln missense_variant 0.96
mmpL5 779472 c.-992G>A upstream_gene_variant 0.97
mmpS5 779523 c.-618T>A upstream_gene_variant 0.97
mmpS5 779538 c.-633A>C upstream_gene_variant 0.95
mmpS5 779539 c.-634C>A upstream_gene_variant 0.94
rplC 801267 c.459A>G synonymous_variant 0.98
rrs 1471851 n.6T>G non_coding_transcript_exon_variant 1.0
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.29
rrs 1472119 n.274G>A non_coding_transcript_exon_variant 0.28
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.88
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.84
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.78
rrs 1472282 n.437T>G non_coding_transcript_exon_variant 0.31
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.29
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.3
rrs 1472293 n.448C>A non_coding_transcript_exon_variant 0.29
rrs 1472297 n.453_465delGTCCGGGTTCTCT non_coding_transcript_exon_variant 0.31
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.32
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.33
rrs 1472332 n.487A>G non_coding_transcript_exon_variant 0.32
rrs 1472333 n.488G>A non_coding_transcript_exon_variant 0.33
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 0.35
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.39
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.38
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.28
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 0.22
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.18
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.21
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.22
rrs 1472448 n.603T>C non_coding_transcript_exon_variant 0.22
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.22
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.45
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.28
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.49
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.2
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.37
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.36
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.17
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.27
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.37
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.33
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.26
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.26
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.37
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.63
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.58
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.52
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.35
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.21
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.21
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.3
rrl 1475992 n.2335T>C non_coding_transcript_exon_variant 0.15
rrl 1475995 n.2338G>C non_coding_transcript_exon_variant 0.24
rrl 1475996 n.2339T>C non_coding_transcript_exon_variant 0.14
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.24
rrl 1476007 n.2350T>C non_coding_transcript_exon_variant 0.24
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.14
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.19
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.34
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.39
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.37
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.35
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.33
rrl 1476207 n.2550T>C non_coding_transcript_exon_variant 0.22
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.23
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.37
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.44
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.22
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.35
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.28
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 0.18
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.17
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.25
fabG1 1673770 p.Ala111Pro missense_variant 0.4
inhA 1674816 c.615T>C synonymous_variant 0.99
tlyA 1917812 c.-128G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
pncA 2289104 c.138A>G synonymous_variant 0.97
embB 4247590 c.1077A>G synonymous_variant 0.96
embB 4247646 p.Glu378Ala missense_variant 0.97
embB 4247815 c.1302C>T synonymous_variant 0.95
ethA 4326463 c.1011C>T synonymous_variant 0.99
ethA 4326740 p.Arg245His missense_variant 0.98
ethA 4326764 p.Ala237Val missense_variant 0.27
gid 4407588 c.615A>G synonymous_variant 0.87
gid 4408185 c.18C>T synonymous_variant 1.0