TB-Profiler result

Run: SRR11972323
Summary

Run ID: SRR11972323

Sample name:

Date: 03-04-2023 05:36:54

Number of reads: 1092931

Percentage reads mapped: 81.03

Strain: lineage1.1.3.2

Drug-resistance: RR-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 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.99
lineage1.1.3.2 Indo-Oceanic NA 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
rpoB 761090 p.Ser428Arg missense_variant 0.12 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.59 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 0.92
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.96
gyrA 8688 p.Ala463Ser missense_variant 0.18
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9465 p.Tyr722His missense_variant 0.1
gyrA 9774 p.Asp825Asn missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575548 c.201C>T synonymous_variant 1.0
mshA 576228 p.Arg294His missense_variant 0.33
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
ccsA 620864 c.974G>T stop_lost&splice_region_variant 0.12
rpoB 760698 p.Lys298Glu missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763042 p.Leu1079Pro missense_variant 0.2
rpoC 763422 p.Glu18Val missense_variant 0.25
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
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 766272 p.Cys968Phe missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776146 p.Ala779Thr missense_variant 0.17
mmpS5 778751 p.Asp52Ala missense_variant 0.17
mmpR5 779207 p.Met73Lys missense_variant 0.12
mmpS5 779679 c.-774G>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303293 c.363G>T synonymous_variant 0.12
fbiC 1303910 p.Pro327Leu missense_variant 0.17
fbiC 1304136 c.1206C>T synonymous_variant 0.15
fbiC 1304347 p.Trp473Arg missense_variant 0.17
fbiC 1304404 p.Asp492Asn missense_variant 0.2
fbiC 1304485 p.Thr519Pro missense_variant 0.29
fbiC 1305345 c.2415C>T synonymous_variant 0.11
embR 1416629 p.Gly240Asp missense_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.12
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.12
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.12
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.44
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.52
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.52
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.51
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.24
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.12
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.12
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.13
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.13
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.2
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.2
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.21
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.46
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.54
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.67
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.68
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.71
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.68
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.62
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.61
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.61
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.56
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.57
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.49
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.25
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.14
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.54
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.65
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.64
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.63
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.61
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.35
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.18
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.37
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.37
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.34
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.39
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.36
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.3
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.35
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.35
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.42
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 0.15
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.15
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.15
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 0.37
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.47
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.44
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.48
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.45
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.15
rrl 1475552 n.1895G>C non_coding_transcript_exon_variant 0.16
rrl 1475574 n.1917C>A non_coding_transcript_exon_variant 0.19
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.23
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.34
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.33
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.52
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.51
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.32
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.29
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.21
rrl 1476126 n.2469C>T non_coding_transcript_exon_variant 0.19
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.19
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.21
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.34
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.22
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.23
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.17
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.18
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.19
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.21
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.21
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.21
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.21
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.2
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.3
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.38
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.53
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.51
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.56
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.59
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.62
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.62
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.54
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.53
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.54
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.53
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.34
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.23
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.2
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.1
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 0.96
PPE35 2168340 p.Ala758Glu missense_variant 0.13
PPE35 2170415 c.198A>G synonymous_variant 0.15
PPE35 2170424 c.189G>C synonymous_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289806 c.-565A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518582 c.468G>A synonymous_variant 1.0
kasA 2519184 p.Leu357Pro missense_variant 0.1
eis 2714243 p.His364Asn missense_variant 0.11
eis 2714964 c.369C>T synonymous_variant 0.33
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726202 c.10C>T synonymous_variant 0.12
folC 2747077 c.522G>A synonymous_variant 0.15
pepQ 2859320 c.1098dupC frameshift_variant 0.12
pepQ 2860092 c.327C>T synonymous_variant 0.13
ribD 2987246 c.408C>T synonymous_variant 0.22
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065855 p.Ala113Thr missense_variant 0.13
thyX 3067488 p.Lys153Arg missense_variant 0.15
thyX 3067811 c.135G>A synonymous_variant 0.15
thyX 3068134 c.-189C>T upstream_gene_variant 0.12
thyA 3074420 p.Lys18Glu missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087549 c.732delC frameshift_variant 0.11
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449724 c.1221C>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474478 p.Val158Leu missense_variant 0.11
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612978 p.Gly47Ser missense_variant 0.12
fbiB 3642173 c.639G>A synonymous_variant 1.0
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0
clpC1 4038897 p.Gly603Asp missense_variant 0.2
clpC1 4040269 p.Gln146Lys missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044165 c.117G>A synonymous_variant 0.12
embC 4239793 c.-70A>T upstream_gene_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240807 c.945C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241925 p.Arg688His missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245809 c.2579delC frameshift_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.3
embB 4246563 p.Leu17Trp missense_variant 0.17
embB 4246567 c.54G>T synonymous_variant 0.18
embB 4246789 c.276A>T synonymous_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248680 p.Val723Met missense_variant 0.13
embB 4248754 c.2241C>T synonymous_variant 0.13
embB 4248781 c.2268G>A synonymous_variant 1.0
aftB 4268288 c.549G>T synonymous_variant 0.25
ubiA 4269085 p.Val250Gly missense_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269495 c.-659G>C upstream_gene_variant 0.12
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4326724 c.-825G>A upstream_gene_variant 0.14
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 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0