TB-Profiler result

Run: SRR5341423
Summary

Run ID: SRR5341423

Sample name:

Date: 04-04-2023 10:20:35

Number of reads: 864363

Percentage reads mapped: 80.57

Strain: lineage1.1.2

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
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.37 streptomycin
gid 4407851 c.351delG 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 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 761879 p.Glu691Asp missense_variant 0.13
rpoC 762371 c.-999G>A upstream_gene_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
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.18
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.18
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.27
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.34
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.4
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.38
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.34
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.35
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.35
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.37
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.32
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.33
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.34
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.22
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.19
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.19
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.17
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.15
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.15
rrs 1472543 n.699_700delCA non_coding_transcript_exon_variant 0.15
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.27
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.26
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.26
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.27
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.26
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.27
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.31
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.3
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.3
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.3
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.22
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.22
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.37
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.36
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.37
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.35
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.26
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.14
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.15
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.16
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.16
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.15
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.15
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.17
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.23
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.27
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.27
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.12
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.13
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.13
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.11
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.21
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.22
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.22
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.23
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.21
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.39
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.4
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.39
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.41
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.37
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.27
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.16
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.13
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.13
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.11
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.11
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.12
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.12
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.12
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.13
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.13
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
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715016 p.Arg106His missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2860398 c.21A>C synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
fbiD 3339465 p.Asp116Glu missense_variant 0.13
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 1.0
clpC1 4038338 c.2364_2366dupGAT disruptive_inframe_insertion 0.74
clpC1 4038738 p.Asp656Gly missense_variant 0.13
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
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