TB-Profiler result

Run: ERR2513738
Summary

Run ID: ERR2513738

Sample name:

Date: 31-03-2023 19:52:23

Number of reads: 840534

Percentage reads mapped: 94.82

Strain: lineage1.1.3.1

Drug-resistance: Other

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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
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.23 streptomycin
gid 4407831 c.371delT 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
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 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491604 c.822G>T synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 762835 p.Gly1010Asp missense_variant 0.17
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
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779526 c.-621G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.1
Rv1258c 1406946 p.Ala132Gly missense_variant 0.1
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.11
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.15
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.14
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.14
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.13
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.14
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.21
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.21
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.19
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.19
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.11
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.11
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.11
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.11
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.22
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.22
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.16
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.21
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.19
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.18
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.19
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.19
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.19
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.17
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.27
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.16
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.33
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.12
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.46
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.2
rrs 1472735 n.890C>G non_coding_transcript_exon_variant 0.12
rrs 1472740 n.895G>C non_coding_transcript_exon_variant 0.12
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.2
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.22
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.35
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.26
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.24
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.46
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.43
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.33
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.4
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.5
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.58
rrs 1472958 n.1113A>C non_coding_transcript_exon_variant 0.52
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.53
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.53
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.55
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.53
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.57
rrs 1472988 n.1143T>G non_coding_transcript_exon_variant 0.55
rrs 1473001 n.1156G>A non_coding_transcript_exon_variant 0.57
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.53
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.55
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.53
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.52
rrs 1473047 n.1202C>T non_coding_transcript_exon_variant 0.46
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.48
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.53
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.43
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.28
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.21
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.21
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.12
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.12
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.12
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.11
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.11
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.12
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.12
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.14
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.14
rrs 1473305 n.1460G>A non_coding_transcript_exon_variant 0.12
rrl 1473993 n.336G>T non_coding_transcript_exon_variant 0.29
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.18
rrl 1474565 n.908T>C non_coding_transcript_exon_variant 0.15
rrl 1476018 n.2361G>T non_coding_transcript_exon_variant 0.22
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.17
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.18
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.1
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.12
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.12
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.12
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.12
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.12
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.11
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.11
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.15
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.15
fabG1 1674166 p.Met243Val missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154868 p.Leu415Pro missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.97
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.22
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 1.0
kasA 2518639 c.525G>A synonymous_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 0.94
Rv2752c 3064632 c.1560C>T synonymous_variant 0.95
Rv2752c 3064997 p.Thr399Ala missense_variant 0.13
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 3474023 p.Ile6Thr missense_variant 0.11
fprA 3474165 c.159C>G synonymous_variant 0.12
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612794 p.Gly108Ala missense_variant 0.11
alr 3841253 c.168C>T 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 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C 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
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0