TB-Profiler result

Run: SRR13861415
Summary

Run ID: SRR13861415

Sample name:

Date: 03-04-2023 09:31:11

Number of reads: 211198

Percentage reads mapped: 5.29

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 0.95 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 6209 c.970C>T synonymous_variant 0.33
gyrB 6223 c.984G>C synonymous_variant 0.25
gyrB 6242 p.Arg335Lys missense_variant 0.29
gyrB 6253 c.1014G>C synonymous_variant 0.29
gyrB 6280 c.1041T>C synonymous_variant 0.33
gyrB 6286 c.1047T>C synonymous_variant 0.4
gyrB 6292 c.1053G>C synonymous_variant 0.4
gyrB 6295 c.1056A>G synonymous_variant 0.4
gyrB 6298 c.1059C>T synonymous_variant 0.4
gyrB 6299 c.1060C>T synonymous_variant 0.4
gyrA 6307 c.-995T>G upstream_gene_variant 0.4
gyrA 6319 c.-983G>C upstream_gene_variant 0.4
gyrA 6325 c.-977C>G upstream_gene_variant 0.4
gyrA 9502 p.Arg734His missense_variant 1.0
rpoB 759681 c.-126C>T upstream_gene_variant 1.0
rpoB 761133 c.1327_1329delTTGinsCTC synonymous_variant 0.2
rpoB 761150 c.1344A>C synonymous_variant 0.2
rpoB 761165 c.1359G>C synonymous_variant 0.25
rpoB 761180 c.1374A>C synonymous_variant 0.25
rpoB 761239 p.Cys478Tyr missense_variant 0.86
rpoB 761249 c.1443A>G synonymous_variant 0.25
rpoB 761255 c.1449T>G synonymous_variant 0.22
rpoB 763243 p.Asp1146Ala missense_variant 0.25
rpoC 764131 c.762T>C synonymous_variant 0.2
rpoC 764161 c.792G>C synonymous_variant 0.2
rpoC 764188 c.819A>G synonymous_variant 0.2
rpoC 764195 p.Ser276Gln missense_variant 0.22
rpoC 764203 c.834G>T synonymous_variant 0.25
rpoC 764206 c.837T>C synonymous_variant 0.29
rpoC 765478 c.2109T>C synonymous_variant 0.15
rpoC 765499 c.2130C>G synonymous_variant 0.15
rpoC 766801 c.3432C>A synonymous_variant 0.25
rpoC 766804 c.3435A>G synonymous_variant 0.25
mmpL5 776185 p.Lys766Glu missense_variant 1.0
mmpL5 779400 c.-920C>A upstream_gene_variant 1.0
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.25
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.25
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.25
rrs 1471970 n.125G>A non_coding_transcript_exon_variant 0.25
rrs 1472028 n.183A>T non_coding_transcript_exon_variant 0.2
rrs 1472030 n.185G>A non_coding_transcript_exon_variant 0.2
rrs 1472031 n.186G>A non_coding_transcript_exon_variant 0.2
rrs 1472034 n.189T>C non_coding_transcript_exon_variant 0.18
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.22
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.44
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.44
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.65
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.79
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.62
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.83
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.83
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.83
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.85
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.85
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.84
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.83
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.83
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.86
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.85
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.85
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.85
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.84
rrs 1472230 n.385C>T non_coding_transcript_exon_variant 0.24
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.84
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.84
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.83
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.76
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.73
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.57
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.52
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.35
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.35
rrs 1472277 n.432C>A non_coding_transcript_exon_variant 0.31
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.43
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.73
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.9
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.9
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.89
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.9
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.89
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.88
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.9
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.9
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.9
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.9
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.9
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.9
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.9
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.9
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.95
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.95
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.95
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.94
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.95
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.94
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.94
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.95
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.95
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.95
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.95
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.95
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.95
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.87
rrs 1472865 n.1020C>G non_coding_transcript_exon_variant 1.0
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.64
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.59
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.59
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.59
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.62
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.62
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.62
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.62
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.64
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.64
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.64
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.67
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.64
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.67
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.67
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.67
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.7
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.7
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.7
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.22
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.22
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.2
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.2
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.18
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.22
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.25
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.29
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.33
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.29
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.33
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.33
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.33
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.33
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.74
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.94
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.96
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.98
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.97
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.98
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.97
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.98
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.98
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.97
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.98
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.98
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.98
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.98
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.98
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.97
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.97
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.97
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.97
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.98
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.99
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.99
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.99
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.99
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.98
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.77
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.98
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.98
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.98
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.98
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.98
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.97
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.96
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.92
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.92
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.92
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.91
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.92
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.92
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.91
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 0.91
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.91
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.92
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.9
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.5
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.33
tlyA 1918063 p.Pro42Ala missense_variant 1.0
ndh 2102985 p.Ile20Val missense_variant 1.0
katG 2155856 p.Thr86Ser missense_variant 1.0
PPE35 2169233 c.1379delT frameshift_variant 1.0
kasA 2517947 c.-168C>T upstream_gene_variant 0.22
kasA 2518783 c.669T>C synonymous_variant 0.2
kasA 2518792 c.678C>G synonymous_variant 0.2
kasA 2518795 c.681C>G synonymous_variant 0.2
Rv2752c 3065376 c.815delT frameshift_variant 1.0
Rv2752c 3066351 c.-160G>T upstream_gene_variant 1.0
thyX 3067731 p.Val72Ala missense_variant 1.0
thyX 3067825 p.Arg41Gly missense_variant 1.0
fbiD 3338949 c.-169_-168insT upstream_gene_variant 1.0
Rv3083 3448707 c.204G>A synonymous_variant 1.0
Rv3083 3449768 p.Thr422Lys missense_variant 1.0
fbiB 3641403 c.-132C>T upstream_gene_variant 1.0
fbiB 3642581 c.1047A>C synonymous_variant 0.4
fbiB 3642593 c.1059G>C synonymous_variant 0.4
fbiB 3642602 c.1068A>C synonymous_variant 0.4
fbiB 3642605 c.1071A>G synonymous_variant 0.4
fbiB 3642614 c.1080C>T synonymous_variant 0.4
fbiB 3642620 c.1086T>C synonymous_variant 0.4
fbiB 3642656 c.1122G>C synonymous_variant 0.4
fbiB 3642659 c.1125C>G synonymous_variant 0.4
fbiB 3642662 c.1128C>G synonymous_variant 0.4
fbiB 3642668 c.1134A>C synonymous_variant 0.33
fbiB 3642677 c.1143A>G synonymous_variant 0.4
fbiB 3642680 c.1146A>G synonymous_variant 0.4
fbiB 3642684 c.1150T>C synonymous_variant 0.33
fbiB 3642694 p.Ala387Gly missense_variant 0.33
fbiB 3642696 c.1162C>T synonymous_variant 0.33
fbiB 3642701 c.1167C>G synonymous_variant 0.33
fbiB 3642710 c.1176G>C synonymous_variant 0.33
alr 3841257 p.His55Leu missense_variant 1.0
rpoA 3877587 c.921A>G synonymous_variant 0.67
rpoA 3877613 p.Ile299Val missense_variant 0.67
rpoA 3877638 c.870T>C synonymous_variant 0.67
rpoA 3878346 c.162T>C synonymous_variant 0.67
rpoA 3878385 c.123C>G synonymous_variant 0.4
rpoA 3878391 c.117T>C synonymous_variant 0.4
rpoA 3878396 c.112C>T synonymous_variant 0.4
rpoA 3878436 c.72A>G synonymous_variant 0.4
rpoA 3878442 c.66G>C synonymous_variant 0.4
rpoA 3878454 c.54A>C synonymous_variant 0.33
rpoA 3878472 p.Asp12Glu missense_variant 0.33
rpoA 3878478 c.30C>G synonymous_variant 0.33
ddn 3986668 c.-176T>C upstream_gene_variant 1.0
clpC1 4038908 c.1797C>G synonymous_variant 0.25
clpC1 4039208 c.1497C>G synonymous_variant 0.22
clpC1 4039226 c.1479T>C synonymous_variant 0.22
clpC1 4039268 c.1437C>G synonymous_variant 0.22
clpC1 4039274 c.1431G>C synonymous_variant 0.2
clpC1 4039391 c.1314T>G synonymous_variant 0.13
clpC1 4039409 c.1296T>C synonymous_variant 0.21
clpC1 4039412 c.1293T>G synonymous_variant 0.13
clpC1 4039448 c.1257A>G synonymous_variant 0.14
clpC1 4039463 c.1242C>G synonymous_variant 0.14
clpC1 4039466 c.1239T>C synonymous_variant 0.14
clpC1 4039481 c.1224T>G synonymous_variant 0.17
clpC1 4039484 c.1221T>G synonymous_variant 0.17
embC 4241864 p.Leu668Met missense_variant 1.0
embB 4245557 c.-957G>A upstream_gene_variant 1.0
embB 4248265 c.1752C>T synonymous_variant 0.18
embB 4248266 c.1753C>T synonymous_variant 0.18
embB 4248277 c.1764G>C synonymous_variant 0.2
embB 4248316 c.1803C>G synonymous_variant 0.2
embB 4248319 c.1806A>G synonymous_variant 0.2
embB 4248322 c.1809G>C synonymous_variant 0.18
embB 4248343 c.1830G>C synonymous_variant 0.2
embB 4248346 c.1833G>C synonymous_variant 0.2
embB 4248350 c.1837T>C synonymous_variant 0.18
embB 4248355 c.1842A>G synonymous_variant 0.18
embB 4248358 c.1845C>G synonymous_variant 0.18
embB 4248361 c.1848A>G synonymous_variant 0.18
embB 4248362 p.Ser617Ala missense_variant 0.18
embB 4248398 c.1885C>T synonymous_variant 0.15
aftB 4268956 c.-120C>T upstream_gene_variant 0.33
ethA 4327092 p.Ala128Pro missense_variant 1.0
gid 4408151 p.Leu18Val missense_variant 1.0