TB-Profiler result

Run: SRR12199410
Summary

Run ID: SRR12199410

Sample name:

Date: 03-04-2023 06:38:02

Number of reads: 361501

Percentage reads mapped: 50.26

Strain: lineage1.1.3

Drug-resistance: Sensitive

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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 0.99
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.97
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
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
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 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.75
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
rpoB 759776 c.-31T>G upstream_gene_variant 0.25
rpoB 761359 p.Val518Ala missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 0.83
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 0.72
rplC 801338 p.Val177Ala missense_variant 0.95
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.4
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.33
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.33
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.38
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.36
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.27
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.17
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.2
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.2
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.2
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.14
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.15
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.15
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.12
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.24
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.24
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.15
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.24
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.21
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.21
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.22
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.22
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.22
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.19
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.19
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.19
rrs 1472679 n.834_835insAC non_coding_transcript_exon_variant 0.19
rrs 1472684 n.841_846delGATCCG non_coding_transcript_exon_variant 0.21
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.27
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.27
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.27
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.29
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.29
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.46
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.5
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.58
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.33
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.18
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.18
rrs 1472953 n.1109_1112delTCTC non_coding_transcript_exon_variant 0.14
rrs 1472959 n.1114_1115insTTTA non_coding_transcript_exon_variant 0.14
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.12
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.18
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.16
rrs 1473093 n.1248C>A non_coding_transcript_exon_variant 0.16
rrs 1473094 n.1249T>A non_coding_transcript_exon_variant 0.16
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.17
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.17
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.17
rrs 1473115 n.1270G>C non_coding_transcript_exon_variant 0.19
rrs 1473121 n.1276_1277insA 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 0.25
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.24
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.25
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.29
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.25
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.24
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.25
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.25
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.31
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.31
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.24
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.21
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.18
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 1.0
rrl 1474479 n.822A>C non_coding_transcript_exon_variant 0.3
rrl 1474482 n.825G>T non_coding_transcript_exon_variant 0.3
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.33
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.33
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.12
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.11
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.11
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.25
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.32
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.29
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.29
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.29
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.29
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.29
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.29
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.29
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.33
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.33
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.33
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.38
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.41
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.53
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.53
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.41
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.31
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.21
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.21
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.27
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.21
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.21
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.21
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.21
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.21
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.21
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.21
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.21
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.21
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.21
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.2
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.2
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.21
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.21
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
inhA 1674883 p.Ile228Val missense_variant 0.91
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
PPE35 2170048 p.Leu189Val missense_variant 0.69
PPE35 2170053 p.Thr187Ser missense_variant 0.69
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.9
kasA 2519048 p.Gly312Ser missense_variant 0.17
eis 2715441 c.-109C>T upstream_gene_variant 0.9
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074132 p.Ala114Thr missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His 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 0.86
fbiB 3642173 c.639G>A synonymous_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 4244859 p.Gly543Arg missense_variant 0.22
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.16
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 4407780 c.423G>A synonymous_variant 0.8
gid 4407873 c.330G>T synonymous_variant 0.9