TB-Profiler result

Run: SRR6045045
Summary

Run ID: SRR6045045

Sample name:

Date: 04-04-2023 11:51:55

Number of reads: 347244

Percentage reads mapped: 22.96

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 0.92 streptomycin
embB 4247652 p.Ser380Asn missense_variant 0.29 ethambutol
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 7071 c.1835delG frameshift_variant 0.17
gyrA 7268 c.-34C>T upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7634 c.333C>T synonymous_variant 0.29
gyrA 7659 p.Gly120Ser missense_variant 0.22
gyrA 7691 c.390C>A synonymous_variant 0.18
gyrA 9152 p.Tyr617* stop_gained 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575693 p.Pro116Thr missense_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576205 c.858G>T synonymous_variant 0.17
mshA 576751 p.Lys468Asn missense_variant 0.5
ccsA 620286 c.396G>T synonymous_variant 0.12
ccsA 620532 c.642T>G synonymous_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.33
rpoB 761182 p.Arg459Leu missense_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763717 c.348T>C synonymous_variant 0.12
rpoC 763732 c.363C>T synonymous_variant 0.13
rpoC 763747 c.378G>A synonymous_variant 0.2
rpoC 763821 p.Leu151Pro missense_variant 0.15
rpoC 765036 p.Arg556Leu missense_variant 0.2
rpoC 765465 p.Asp699Val missense_variant 0.22
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 767286 p.Pro1306Gln missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775706 p.Met925Ile missense_variant 0.17
mmpL5 775834 p.Ala883Ser missense_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.4
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781891 p.Lys111Ile missense_variant 0.18
rpsL 781901 c.342C>T synonymous_variant 0.2
fbiC 1302852 c.-79C>T upstream_gene_variant 0.14
fbiC 1303016 p.Val29Gly missense_variant 0.2
fbiC 1303370 p.Leu147Pro missense_variant 0.2
fbiC 1305450 c.2520C>A synonymous_variant 0.25
Rv1258c 1406093 c.1248A>C synonymous_variant 0.25
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 0.4
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.4
rrs 1471900 n.55C>T non_coding_transcript_exon_variant 0.4
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.36
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.33
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.31
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.31
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.25
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.33
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.33
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.3
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.3
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.5
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.53
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.53
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.62
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.31
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.15
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.4
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.4
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.4
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.29
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.29
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.29
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.56
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.8
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.79
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.79
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.79
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.81
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.84
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.85
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.85
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.88
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.91
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.91
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.9
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.85
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.85
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.85
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.69
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.67
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.72
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.72
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.72
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.72
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.72
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.81
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.86
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.9
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.9
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.9
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.91
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.95
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.94
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.5
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.58
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.67
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.57
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.57
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.4
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.4
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.2
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.17
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.17
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.17
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.17
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.25
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.2
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.33
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.24
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.24
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.21
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.21
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.15
rrl 1473503 n.-155G>A upstream_gene_variant 0.14
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.4
rrl 1474016 n.359C>G non_coding_transcript_exon_variant 0.4
rrl 1474022 n.365G>A non_coding_transcript_exon_variant 0.4
rrl 1474044 n.387C>T non_coding_transcript_exon_variant 0.4
rrl 1474045 n.388C>T non_coding_transcript_exon_variant 0.4
rrl 1474053 n.396G>A non_coding_transcript_exon_variant 0.4
rrl 1474054 n.397T>C non_coding_transcript_exon_variant 0.4
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.67
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.8
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.8
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.8
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.67
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 0.33
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.33
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.33
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.33
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.33
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.33
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.5
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.5
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.42
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.54
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.54
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.57
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.57
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.25
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.25
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.88
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.88
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.88
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.95
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.88
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.88
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.88
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.86
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 1.0
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 1.0
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 1.0
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 1.0
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 1.0
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 1.0
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 1.0
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 1.0
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 1.0
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 1.0
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.89
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.9
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.88
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.89
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.9
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.9
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.95
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.98
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.82
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.64
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834320 p.Val260Asp missense_variant 0.18
rpsA 1834345 c.804C>T synonymous_variant 0.17
rpsA 1834348 c.807T>C synonymous_variant 0.17
rpsA 1834361 c.820T>C synonymous_variant 0.17
rpsA 1834366 c.825A>G synonymous_variant 0.17
rpsA 1834387 c.846C>T synonymous_variant 0.29
rpsA 1834396 c.855G>T synonymous_variant 0.29
rpsA 1834411 c.870T>C synonymous_variant 0.25
rpsA 1834423 c.882G>T synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102122 c.921C>A synonymous_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154954 c.1158G>T synonymous_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168849 c.1764G>A synonymous_variant 0.33
PPE35 2170595 p.Leu6Phe missense_variant 0.29
Rv1979c 2221755 c.1410C>A synonymous_variant 0.12
Rv1979c 2223266 c.-102G>T upstream_gene_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289377 c.-136A>G upstream_gene_variant 0.22
kasA 2519006 p.Ala298Ser missense_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.25
ahpC 2726338 p.Val49Gly missense_variant 0.29
folC 2747707 c.-109C>A upstream_gene_variant 0.29
pepQ 2859382 p.Gly346Val missense_variant 0.18
Rv2752c 3065655 c.537C>T synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.17
ald 3087109 p.Leu97* stop_gained 0.17
fbiD 3339688 p.Thr191Pro missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841115 c.306T>C synonymous_variant 0.25
rpoA 3878115 p.Lys131Asn missense_variant 0.25
rpoA 3878276 p.Leu78Met missense_variant 0.18
clpC1 4039594 p.Arg371Gly missense_variant 0.29
clpC1 4039602 p.Ala368Val missense_variant 0.29
panD 4044429 c.-148C>T upstream_gene_variant 0.33
embC 4240139 p.Gly93Arg missense_variant 0.12
embC 4240585 c.725delG frameshift_variant 0.29
embC 4240646 p.Phe262Val missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242846 p.Arg995Leu missense_variant 0.25
embA 4242856 c.-377C>A upstream_gene_variant 0.22
embC 4243047 p.Arg1062Gln missense_variant 0.29
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4245887 c.-627T>C upstream_gene_variant 0.12
embB 4246416 c.-98C>A upstream_gene_variant 0.17
embB 4248562 c.2049G>A synonymous_variant 0.5
aftB 4267341 p.Gly499Val missense_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268421 p.Leu139Pro missense_variant 0.17
ethR 4326670 c.-879G>T upstream_gene_variant 0.14
ethA 4326856 p.Gln206His missense_variant 0.4
ethA 4327827 c.-354A>G upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408440 c.-238C>A upstream_gene_variant 0.15