TB-Profiler result

Run: SRR13861362
Summary

Run ID: SRR13861362

Sample name:

Date: 03-04-2023 09:29:52

Number of reads: 1074214

Percentage reads mapped: 53.77

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 1472733 n.888G>A non_coding_transcript_exon_variant 0.46 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
gyrB 5807 p.Val190Phe missense_variant 1.0
gyrA 6898 c.-404G>C upstream_gene_variant 1.0
gyrA 8039 c.738T>C synonymous_variant 1.0
mshA 575293 c.-55T>A upstream_gene_variant 1.0
mshA 575414 p.Gly23Ser missense_variant 1.0
rpoC 763642 c.273G>C synonymous_variant 0.15
rpoC 763660 c.291T>G synonymous_variant 0.11
rpoC 765007 c.1638T>G synonymous_variant 0.13
rpoC 765124 c.1755G>C synonymous_variant 0.97
fbiC 1303686 c.756C>G synonymous_variant 0.12
fbiC 1303695 c.765T>C synonymous_variant 0.12
fbiC 1303728 c.798G>A synonymous_variant 0.11
fbiC 1303730 p.Leu267Pro missense_variant 0.12
fbiC 1303732 p.Ser268Ala missense_variant 0.12
fbiC 1303746 c.816T>C synonymous_variant 0.12
fbiC 1303749 c.819G>C synonymous_variant 0.12
fbiC 1303752 c.822A>G synonymous_variant 0.13
fbiC 1303755 c.825T>C synonymous_variant 0.13
fbiC 1303785 c.855G>C synonymous_variant 0.13
fbiC 1303789 p.Ile287Val missense_variant 0.13
fbiC 1303818 c.888C>G synonymous_variant 0.15
fbiC 1303854 c.924T>C synonymous_variant 0.14
fbiC 1303860 c.930A>C synonymous_variant 0.14
fbiC 1303881 c.951G>C synonymous_variant 0.12
fbiC 1303884 c.954T>G synonymous_variant 0.12
fbiC 1303911 c.981G>C synonymous_variant 0.13
fbiC 1303914 c.984C>G synonymous_variant 0.12
fbiC 1303920 c.990C>G synonymous_variant 0.13
fbiC 1303929 c.999G>C synonymous_variant 0.14
fbiC 1303947 c.1017T>C synonymous_variant 0.14
fbiC 1303948 p.Gly340Arg missense_variant 0.14
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.27
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.19
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.31
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.3
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.31
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.32
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.34
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.31
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.29
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.29
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.29
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.29
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.29
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.3
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.29
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.29
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.29
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.29
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.22
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.17
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.2
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.37
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.38
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.36
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.38
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.38
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.39
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.41
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.43
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.43
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.44
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.41
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.41
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.41
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.42
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.47
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.48
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.49
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.43
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.43
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.43
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.46
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.41
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.42
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.43
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.46
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.46
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.25
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.44
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.5
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.56
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.55
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.54
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.55
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.55
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.55
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.53
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.54
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.54
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.54
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.54
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.54
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.54
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.54
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.54
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.56
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.67
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.72
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.73
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.74
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.74
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.72
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.56
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.72
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.71
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.72
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.72
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.74
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.71
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.58
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.5
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.45
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.45
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.44
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.43
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.43
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.43
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.44
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.44
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.45
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.46
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.4
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.42
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.42
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.35
rpsA 1834248 p.His236Leu missense_variant 0.94
katG 2154449 p.Ala555Ser missense_variant 1.0
PPE35 2170218 p.Ala132Glu missense_variant 1.0
eis 2715396 c.-65delT upstream_gene_variant 1.0
ribD 2987136 p.Val100Ile missense_variant 1.0
ribD 2987590 p.Leu251Arg missense_variant 1.0
Rv2752c 3064996 p.Thr399Asn missense_variant 1.0
thyA 3073953 c.519T>C synonymous_variant 0.12
thyA 3074031 c.441T>C synonymous_variant 0.12
alr 3841281 p.His47Arg missense_variant 1.0
clpC1 4039292 c.1413C>A synonymous_variant 1.0
clpC1 4039426 p.Lys427Gln missense_variant 0.97
embA 4243228 c.-5G>T upstream_gene_variant 1.0
embA 4243540 p.Ala103Asp missense_variant 1.0
embA 4244146 p.Asp305Ala missense_variant 1.0
embB 4249506 c.2994delG frameshift_variant 0.93