TB-Profiler result

Run: SRR11972394
Summary

Run ID: SRR11972394

Sample name:

Date: 03-04-2023 05:40:06

Number of reads: 951278

Percentage reads mapped: 88.93

Strain: lineage2.2.1.1

Drug-resistance: Pre-XDR-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 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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.42 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247729 p.Gly406Cys missense_variant 1.0 ethambutol
ethA 4326589 c.884delT frameshift_variant 0.29 ethionamide, ethionamide
ethA 4326882 c.587_591delACTCG frameshift_variant 0.88 ethionamide
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
pncA 2277357 c.-1108_*11323del transcript_ablation 1.0 pyrazinamide
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761658 p.Pro618Thr missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_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 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 1472507 n.662C>G non_coding_transcript_exon_variant 0.12
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.15
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.17
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.22
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.23
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.23
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.23
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.26
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.25
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.24
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.24
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.28
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.34
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.38
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.37
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.37
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.34
rrs 1472676 n.832_840delCTTCCTTGG non_coding_transcript_exon_variant 0.34
rrs 1472689 n.844C>G non_coding_transcript_exon_variant 0.33
rrs 1472690 n.845_846insCCTTA non_coding_transcript_exon_variant 0.34
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.34
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.34
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.34
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.36
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.38
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.44
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.44
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.17
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.11
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.14
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.15
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.16
rrs 1473080 n.1235C>A non_coding_transcript_exon_variant 0.11
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.11
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.2
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.21
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.21
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.21
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.17
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.17
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.17
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.17
rrs 1473131 n.1286G>T non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.16
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.16
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.16
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.16
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.17
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.17
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.17
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.17
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.16
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.17
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.19
rrl 1474527 n.870T>G non_coding_transcript_exon_variant 0.15
rrl 1474528 n.871T>C non_coding_transcript_exon_variant 0.15
rrl 1474530 n.873G>T non_coding_transcript_exon_variant 0.15
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.15
rrl 1474539 n.882C>A non_coding_transcript_exon_variant 0.15
rrl 1474542 n.885A>C non_coding_transcript_exon_variant 0.15
rrl 1474552 n.895C>G non_coding_transcript_exon_variant 0.16
rrl 1474570 n.913G>T non_coding_transcript_exon_variant 0.21
rrl 1474578 n.921A>G non_coding_transcript_exon_variant 0.21
rrl 1474584 n.927C>G non_coding_transcript_exon_variant 0.26
rrl 1474586 n.929T>A non_coding_transcript_exon_variant 0.26
rrl 1474587 n.930G>A non_coding_transcript_exon_variant 0.26
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.16
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.16
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.12
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.1
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.26
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.32
rrl 1475722 n.2065G>A non_coding_transcript_exon_variant 0.35
rrl 1475751 n.2094C>G non_coding_transcript_exon_variant 0.33
rrl 1475752 n.2095C>G non_coding_transcript_exon_variant 0.33
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.33
rrl 1475758 n.2101A>T non_coding_transcript_exon_variant 0.34
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.34
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.34
rrl 1475765 n.2108A>C non_coding_transcript_exon_variant 0.35
rrl 1475769 n.2112T>A non_coding_transcript_exon_variant 0.34
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.33
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.33
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.33
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.29
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.3
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.29
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.3
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.31
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.21
rrl 1475869 n.2212C>T non_coding_transcript_exon_variant 0.16
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.14
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.16
rrl 1476164 n.2507A>C non_coding_transcript_exon_variant 0.16
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.17
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.16
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.16
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.16
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.16
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.16
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.15
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.15
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.15
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.14
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.14
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.14
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.18
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.17
rrl 1476229 n.2572C>A non_coding_transcript_exon_variant 0.2
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.35
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.37
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.31
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.3
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.29
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.31
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.29
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.28
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.27
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.27
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.26
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.26
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.28
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.42
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.43
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.44
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.46
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.45
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.45
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.42
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.46
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.48
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.54
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.54
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.49
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.43
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.46
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.43
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.43
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.45
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.42
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.41
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.41
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.4
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.39
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.35
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.29
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.29
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.28
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.27
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.2
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.17
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.13
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
PPE35 2170048 p.Leu189Val missense_variant 0.24
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474379 p.Ala125Thr missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249329 p.Met939Arg missense_variant 0.18
aftB 4267647 p.Asp397Gly 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