TB-Profiler result

Run: SRR13861568
Summary

Run ID: SRR13861568

Sample name:

Date: 03-04-2023 09:35:02

Number of reads: 107834

Percentage reads mapped: 10.79

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 0.94 streptomycin
ethA 4326568 c.905delT frameshift_variant 1.0 ethionamide
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 7532 c.231T>C synonymous_variant 0.5
gyrA 8820 p.Asp507His missense_variant 1.0
mshA 575967 p.Val207Asp missense_variant 1.0
rpoB 759961 p.Thr52Asn missense_variant 1.0
rpoB 762008 c.2202C>G synonymous_variant 0.29
rpoB 762014 c.2208C>T synonymous_variant 0.29
rpoB 762017 c.2211A>G synonymous_variant 0.33
rpoB 762027 c.2221_2223delCTCinsTTG synonymous_variant 0.33
rpoB 762032 c.2226C>G synonymous_variant 0.33
rpoB 762035 c.2229G>C synonymous_variant 0.33
rpoB 762053 c.2247T>C synonymous_variant 0.33
rpoB 762062 c.2256T>C synonymous_variant 0.33
rpoB 762065 c.2259T>C synonymous_variant 0.33
rpoB 762167 c.2361T>C synonymous_variant 0.4
rpoB 762176 c.2370T>C synonymous_variant 0.4
rpoB 762185 c.2379G>C synonymous_variant 0.4
rpoB 762218 c.2412T>G synonymous_variant 0.4
rpoB 762254 c.2448T>C synonymous_variant 0.4
rpoB 762266 c.2460T>C synonymous_variant 0.4
rpoB 762284 c.2478G>C synonymous_variant 0.4
rpoC 766483 c.3114G>C synonymous_variant 0.29
rpoC 766484 p.Val1039Ile missense_variant 0.29
rpoC 766492 c.3123T>C synonymous_variant 0.29
rpoC 766495 c.3126C>T synonymous_variant 0.29
rpoC 766543 c.3174C>T synonymous_variant 0.33
rpoC 766549 c.3180G>C synonymous_variant 0.33
rpoC 766573 c.3204T>C synonymous_variant 0.33
rpoC 766583 p.Gly1072Ser missense_variant 0.29
rpoC 766588 c.3219G>A synonymous_variant 0.29
rpoC 766591 c.3222A>G synonymous_variant 0.29
rpoC 766594 c.3225G>C synonymous_variant 0.25
rpoC 766607 p.Ile1080Leu missense_variant 0.25
rpoC 766900 c.3531T>C synonymous_variant 0.5
mmpL5 775701 p.Pro927Gln missense_variant 1.0
mmpL5 778828 c.-348G>A upstream_gene_variant 1.0
rplC 801353 p.Val182Ala missense_variant 1.0
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.5
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.5
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.71
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.88
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.68
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.89
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.89
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.9
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.9
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.9
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.95
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 1.0
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 1.0
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 1.0
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 1.0
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 1.0
rrs 1472230 n.385C>T non_coding_transcript_exon_variant 0.26
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.95
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.95
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.95
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.93
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.92
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.88
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.8
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.4
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.67
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.86
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.86
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.86
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.86
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.83
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.83
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.86
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.87
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.87
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.87
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.87
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.87
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.87
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.87
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.91
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.92
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.91
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.89
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.88
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.91
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.91
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.94
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.91
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.94
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.94
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.94
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.94
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.85
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.54
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.62
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.57
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.57
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.57
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.57
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.57
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.54
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.54
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.5
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.5
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.5
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.43
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.5
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.5
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.46
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.5
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.5
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.5
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.62
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.71
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.82
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.79
rrl 1476263 n.2606C>T non_coding_transcript_exon_variant 0.21
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.79
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.82
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.82
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.82
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.79
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.81
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.81
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.81
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.78
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.81
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.81
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.85
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.85
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.86
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.9
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.96
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.96
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.97
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.97
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.97
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.73
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.96
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.97
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.97
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.97
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.97
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.96
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.93
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.91
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.9
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.9
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.9
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.9
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.9
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.92
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.92
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.92
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.92
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.92
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.88
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.9
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.9
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.88
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.5
rpsA 1834175 p.Arg212* stop_gained 1.0
rpsA 1834366 c.825A>G synonymous_variant 0.2
rpsA 1834375 c.834G>A synonymous_variant 0.2
Rv1979c 2222085 c.1080G>C synonymous_variant 1.0
folC 2746135 c.1464A>C stop_lost&splice_region_variant 1.0
ald 3087218 p.Met133Ile missense_variant 1.0
clpC1 4038596 c.2109A>G synonymous_variant 0.33
clpC1 4039145 c.1560G>C synonymous_variant 0.25
clpC1 4040066 c.639G>T synonymous_variant 1.0
embC 4241259 c.1397_1398insT frameshift_variant 1.0
embA 4243358 c.126C>T synonymous_variant 1.0
embA 4243469 c.237C>T synonymous_variant 1.0
embB 4248085 c.1572T>C synonymous_variant 0.18
embB 4248097 c.1584C>G synonymous_variant 0.2
embB 4248206 p.Ser565Gly missense_variant 0.2
embB 4248220 c.1707A>G synonymous_variant 0.22
embB 4248436 c.1923C>T synonymous_variant 1.0