TB-Profiler result

Run: SRR13591377
Summary

Run ID: SRR13591377

Sample name:

Date: 03-04-2023 09:04:37

Number of reads: 584543

Percentage reads mapped: 12.3

Strain: lineage4.1.1.3

Drug-resistance: Sensitive

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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
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 5256 p.Lys6Arg missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7690 p.Thr130Ile missense_variant 0.13
gyrA 7780 p.Val160Glu missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575964 p.Val206Asp missense_variant 0.11
mshA 576578 p.Gly411Trp missense_variant 0.15
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417065 c.281_282dupTG frameshift_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.22
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.55
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.64
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.68
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.7
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.73
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.76
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.83
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.78
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.78
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.75
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.74
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.74
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.74
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.74
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.12
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.12
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.17
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.19
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.16
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.15
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.32
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.33
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.59
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.69
rrs 1472553 n.708C>T non_coding_transcript_exon_variant 0.77
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.75
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.74
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.74
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.73
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.73
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.73
rrs 1472584 n.739A>G non_coding_transcript_exon_variant 0.73
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.77
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.77
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.76
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.23
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.59
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.59
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.61
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.63
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.91
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.91
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.9
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.89
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.29
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.58
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.63
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.71
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.77
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.77
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.79
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.8
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.8
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.78
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.78
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.8
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.8
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.12
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.14
rrl 1474221 n.564T>C non_coding_transcript_exon_variant 0.13
rrl 1474228 n.571T>A non_coding_transcript_exon_variant 0.14
rrl 1475491 n.1834C>T non_coding_transcript_exon_variant 0.24
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.62
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.64
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.64
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.62
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.62
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.62
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.64
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.61
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.58
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.57
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.57
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.57
rrl 1475596 n.1939G>C non_coding_transcript_exon_variant 0.2
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.1
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.21
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.22
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.2
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.31
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.89
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.9
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.89
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.9
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.9
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.89
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.91
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.91
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.91
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.91
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.93
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.94
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.93
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.93
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.92
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.92
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.91
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.91
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.91
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.92
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.76
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.53
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918081 p.Asp48Asn missense_variant 1.0
tlyA 1918655 p.Tyr239Cys missense_variant 0.13
PPE35 2169802 p.Asn271Tyr missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289017 c.225T>C synonymous_variant 1.0
thyX 3067640 c.306G>A synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339631 p.Arg172Cys missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244728 p.Phe499Ser missense_variant 0.18
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249480 c.2967G>T synonymous_variant 0.17
aftB 4268237 p.Met200Ile missense_variant 0.13
aftB 4268498 c.339T>C synonymous_variant 0.15
ubiA 4269195 p.Tyr213* stop_gained 0.14
ubiA 4269440 p.Leu132Ile missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0