TB-Profiler result

Run: SRR22424743
Summary

Run ID: SRR22424743

Sample name:

Date: 04-04-2023 04:09:45

Number of reads: 1005936

Percentage reads mapped: 94.31

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
gyrA 7570 p.Ala90Val missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Arg missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4408087 c.115delC frameshift_variant 1.0 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>G synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.33
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.5
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.4
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.5
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 0.5
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.5
rrs 1472427 n.582T>G non_coding_transcript_exon_variant 0.5
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.67
rrs 1472436 n.591G>T non_coding_transcript_exon_variant 0.67
rrs 1472437 n.592T>G non_coding_transcript_exon_variant 0.67
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.67
rrs 1472448 n.603T>C non_coding_transcript_exon_variant 1.0
rrs 1472449 n.604C>T non_coding_transcript_exon_variant 1.0
rrs 1472450 n.605A>C non_coding_transcript_exon_variant 1.0
rrs 1472451 n.606C>T non_coding_transcript_exon_variant 1.0
rrs 1472462 n.617T>G non_coding_transcript_exon_variant 1.0
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 1.0
rrs 1472473 n.628G>T non_coding_transcript_exon_variant 1.0
rrs 1472474 n.629C>G non_coding_transcript_exon_variant 1.0
rrs 1472476 n.631A>G non_coding_transcript_exon_variant 1.0
rrs 1472484 n.639A>T non_coding_transcript_exon_variant 0.67
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.67
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.67
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.67
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.5
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.5
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.6
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.5
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.5
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.29
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.25
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.25
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.25
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.25
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.29
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.29
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.25
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.22
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.22
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.2
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.2
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.2
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.2
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.2
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.2
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.2
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.22
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.22
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.22
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.22
rrl 1473635 n.-23A>G upstream_gene_variant 1.0
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 1.0
rrl 1474709 n.1052G>A non_coding_transcript_exon_variant 1.0
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 1.0
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 1.0
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 1.0
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 1.0
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 1.0
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 1.0
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 1.0
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 1.0
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 1.0
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.4
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.5
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.5
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.5
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.5
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.5
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.5
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.5
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.5
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.4
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.4
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.4
rrl 1476255 n.2598A>G non_coding_transcript_exon_variant 0.4
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.4
rrl 1476268 n.2611A>G non_coding_transcript_exon_variant 0.4
rrl 1476275 n.2618T>C non_coding_transcript_exon_variant 0.4
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 0.4
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.4
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.4
rrl 1476290 n.2636_2637insCATGGC non_coding_transcript_exon_variant 0.4
rrl 1476295 n.2639_2644delCCCCGA non_coding_transcript_exon_variant 0.4
rrl 1476306 n.2649A>G non_coding_transcript_exon_variant 0.4
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.4
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.4
rrl 1476311 n.2654G>T non_coding_transcript_exon_variant 0.4
rrl 1476312 n.2655T>G non_coding_transcript_exon_variant 0.4
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.5
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.33
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.25
fabG1 1673280 c.-160C>G upstream_gene_variant 0.98
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 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288814 p.Ala143Val missense_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449455 p.Thr318Ala missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.97
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0