TB-Profiler result

Run: SRR6982400

Summary

Run ID: SRR6982400

Sample name:

Date: 04-04-2023 18:36:19

Number of reads: 683050

Percentage reads mapped: 43.84

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 0.64 streptomycin
tlyA 1918529 c.592delG frameshift_variant 0.15 capreomycin
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7440 p.Gly47Trp missense_variant 0.17
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490836 c.54C>T synonymous_variant 0.12
fgd1 490870 p.His30Asn missense_variant 0.13
fgd1 491139 p.Glu119Asp missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575499 c.154delG frameshift_variant 0.18
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576253 c.906G>T synonymous_variant 0.33
mshA 576410 p.Phe355Leu missense_variant 0.12
mshA 576586 c.1239G>T synonymous_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759887 c.81C>A synonymous_variant 0.12
rpoB 762320 c.2514C>G synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764532 p.Gly388Ala missense_variant 0.14
rpoC 764987 p.Gln540Lys missense_variant 0.12
rpoC 765214 c.1845G>A synonymous_variant 0.12
rpoC 766421 p.Gly1018Cys missense_variant 0.13
rpoC 766542 p.Gly1058Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776121 p.Ile787Thr missense_variant 0.11
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777314 p.Trp389* stop_gained 0.25
mmpL5 777371 c.1110C>A synonymous_variant 0.14
mmpL5 777727 p.Phe252Leu missense_variant 0.12
mmpL5 778284 p.Pro66His missense_variant 0.14
mmpR5 779204 p.Arg72Gln missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303850 p.Pro307His missense_variant 0.17
fbiC 1303992 p.Trp354Cys missense_variant 0.15
Rv1258c 1406304 p.Gly346Val missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471878 n.33C>T non_coding_transcript_exon_variant 0.19
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.3
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.37
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.4
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.4
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.41
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.51
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.61
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.61
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.64
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.66
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.66
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.63
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.54
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.53
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.53
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.47
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.38
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.38
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.38
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.23
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.19
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.16
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.16
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.12
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.19
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.32
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.32
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.33
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.33
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.34
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.34
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.39
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 0.43
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.49
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.5
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.5
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.52
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.55
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.47
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.38
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.39
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.36
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.39
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.35
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.35
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.44
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.43
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.64
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.63
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.52
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.44
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.3
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.28
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.19
rrs 1473054 n.1209C>T non_coding_transcript_exon_variant 0.18
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.18
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.18
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.18
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.18
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.2
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.23
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.36
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.23
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.23
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.23
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.23
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.27
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.23
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.16
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.14
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.14
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.14
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.17
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.17
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.15
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.15
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.17
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.17
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.17
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.23
rrl 1473404 n.-254C>A upstream_gene_variant 0.13
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.17
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.17
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.2
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.2
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.2
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.17
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.17
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.17
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.17
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.38
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.4
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.12
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.11
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.14
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.14
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.65
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.68
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.74
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.73
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.73
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.74
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.72
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.72
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.7
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.7
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.7
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.69
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.69
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.69
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.69
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.72
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.72
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.73
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.85
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.87
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.89
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.88
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.88
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.88
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.88
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.89
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.89
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.89
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.9
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.89
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.87
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.82
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.72
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.67
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.67
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.65
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.65
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.65
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.67
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.65
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.67
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.67
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.71
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.64
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.6
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.6
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.45
rrl 1476743 n.3086A>G non_coding_transcript_exon_variant 0.12
fabG1 1673473 p.Pro12Thr missense_variant 0.15
fabG1 1673494 p.Leu19Met missense_variant 0.12
inhA 1674466 p.Asp89Asn missense_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155040 p.Gly358Arg missense_variant 0.2
katG 2155782 c.327_329delTGC disruptive_inframe_deletion 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289370 c.-129C>A upstream_gene_variant 0.12
pncA 2289771 c.-530C>A upstream_gene_variant 0.17
kasA 2518389 c.277_278delCA frameshift_variant 0.12
kasA 2518873 c.759C>T synonymous_variant 0.15
kasA 2518954 c.840C>A synonymous_variant 0.12
eis 2714829 c.504C>A synonymous_variant 0.18
folC 2747044 c.554dupA frameshift_variant 0.25
folC 2747101 c.498G>T synonymous_variant 0.33
pepQ 2859605 p.Gly272Trp missense_variant 0.13
Rv2752c 3064674 c.1518C>A synonymous_variant 0.13
Rv2752c 3065068 p.His375Arg missense_variant 0.13
thyX 3067342 p.Glu202* stop_gained 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087377 c.559delG frameshift_variant 0.18
fbiD 3339378 c.261C>T synonymous_variant 0.17
Rv3083 3448606 p.Leu35Met missense_variant 0.14
Rv3083 3449105 p.Pro201Arg missense_variant 0.33
Rv3083 3449573 p.Arg357Pro missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474618 p.Gln204His missense_variant 0.17
Rv3236c 3612293 p.Phe275Cys missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3877740 c.768G>C synonymous_variant 0.12
ddn 3986759 c.-85C>A upstream_gene_variant 0.12
clpC1 4038258 p.Ala816Val missense_variant 0.22
clpC1 4039407 p.Arg433Gln missense_variant 0.15
clpC1 4039522 p.Leu395Met missense_variant 0.12
clpC1 4040245 p.Gly154Arg missense_variant 0.15
panD 4044314 c.-33C>A upstream_gene_variant 0.14
embC 4239723 c.-140C>A upstream_gene_variant 0.13
embC 4240198 p.Gln112His missense_variant 0.15
embA 4242346 c.-887C>T upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243466 c.234C>A synonymous_variant 0.22
embA 4243575 p.Val115Ile missense_variant 0.14
embA 4244411 p.Trp393* stop_gained 0.15
embA 4245323 p.Met697Ile missense_variant 0.15
embB 4246686 p.Trp58Ser missense_variant 0.17
embB 4247458 p.Tyr315* stop_gained 0.11
embB 4248763 c.2250C>A synonymous_variant 0.12
embB 4249607 p.Thr1032Pro missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267763 c.1074C>A synonymous_variant 0.13
aftB 4268170 p.Ala223Ser missense_variant 0.12
ethA 4327451 p.Val8Asp missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408367 c.-165G>T upstream_gene_variant 0.11