TB-Profiler result

Run: ERR5865119
Summary

Run ID: ERR5865119

Sample name:

Date: 01-04-2023 23:48:26

Number of reads: 994423

Percentage reads mapped: 50.49

Strain: lineage2.2.1

Drug-resistance: MDR-TB

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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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288818 p.Thr142Ala missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide, 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8175 p.Arg292Gly missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490822 p.Gln14Lys missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766023 p.Ile885Thr missense_variant 1.0
rpoC 766641 p.His1091Pro missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779574 c.-669T>C upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.27
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.54
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.53
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.53
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.56
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.54
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.54
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.49
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.49
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.27
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.15
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.15
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.12
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.12
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.12
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.83
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.9
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.9
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.94
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.93
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.92
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.92
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.92
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.95
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.95
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.95
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.95
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.95
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.93
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.67
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.29
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.34
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.45
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.82
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.84
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.93
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.93
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.93
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.94
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.93
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.92
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.62
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.37
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.35
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.35
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.79
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.78
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.78
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.77
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.77
rrs 1473080 n.1235C>A non_coding_transcript_exon_variant 0.78
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.77
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.75
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.74
rrs 1473111 n.1266A>T non_coding_transcript_exon_variant 0.47
rrs 1473115 n.1270G>C non_coding_transcript_exon_variant 0.28
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.16
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.44
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.57
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.56
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.57
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.61
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.65
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.64
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.64
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.71
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.71
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.65
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.57
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.42
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.12
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.19
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.19
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.17
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.14
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.24
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.24
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.4
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.38
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.37
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.37
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.23
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.8
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.8
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.81
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.81
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.81
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.8
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.8
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.8
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.8
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.79
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.79
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.8
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.8
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.75
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.78
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.8
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.8
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 0.81
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 0.84
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.84
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.85
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.94
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.96
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.95
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.95
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.96
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.96
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.97
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.96
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.97
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.96
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.93
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.9
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.74
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.39
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066010 p.Leu61Arg missense_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640855 p.Gly105Arg missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 1.0
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