TB-Profiler result

Run: SRR5818441
Summary

Run ID: SRR5818441

Sample name:

Date: 04-04-2023 11:30:32

Number of reads: 492943

Percentage reads mapped: 99.43

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 1472307 n.462C>T non_coding_transcript_exon_variant 0.23 streptomycin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.67 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 7585 p.Ser95Thr missense_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.95
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.84
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.7
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.22
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.19
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.19
rrs 1472296 n.454_458delTCCGG non_coding_transcript_exon_variant 0.21
rrs 1472303 n.458G>C non_coding_transcript_exon_variant 0.21
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.33
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.32
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.14
rrs 1472332 n.487A>G non_coding_transcript_exon_variant 0.14
rrs 1472333 n.488G>A non_coding_transcript_exon_variant 0.14
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 0.15
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.47
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.19
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.21
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.16
rrs 1472431 n.586G>A non_coding_transcript_exon_variant 0.24
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.3
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.3
rrs 1472439 n.594C>T non_coding_transcript_exon_variant 0.25
rrs 1472447 n.602C>T non_coding_transcript_exon_variant 0.26
rrs 1472448 n.603T>C non_coding_transcript_exon_variant 0.31
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.26
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.32
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.28
rrs 1472484 n.639A>T non_coding_transcript_exon_variant 0.28
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.23
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.21
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.18
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.4
rrs 1472504 n.659A>T non_coding_transcript_exon_variant 0.17
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.17
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.8
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.8
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.4
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.67
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.33
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.19
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.71
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.82
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.14
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.32
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.68
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.17
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.79
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.52
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.22
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.22
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.22
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.2
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.3
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.3
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.33
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.33
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.22
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.22
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.22
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.22
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.22
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.29
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.29
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.97
ahpC 2726389 p.Ala66Val missense_variant 0.15
ahpC 2726648 c.456T>C synonymous_variant 0.18
ahpC 2726701 p.Ser170Phe missense_variant 0.22
ethA 4326764 p.Ala237Val missense_variant 0.22
gid 4407588 c.615A>G synonymous_variant 0.95