TB-Profiler result

Run: ERR4821829
Summary

Run ID: ERR4821829

Sample name:

Date: 01-04-2023 17:28:38

Number of reads: 3555422

Percentage reads mapped: 97.57

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 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 0.39 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 775979 c.2502G>A synonymous_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 1472108 n.263C>T non_coding_transcript_exon_variant 0.15
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.18
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.18
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.19
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.31
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.31
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.26
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.12
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.29
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.13
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.12
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.13
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.13
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.32
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.36
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.36
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.38
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.45
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.43
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.29
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.44
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.44
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.26
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.16
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.24
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.39
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.38
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.18
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.3
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.23
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.17
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.14
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.33
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.3
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.32
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.36
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.25
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrl 1473615 n.-43G>C upstream_gene_variant 1.0
rrl 1474448 n.791T>C non_coding_transcript_exon_variant 0.2
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.38
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.29
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.29
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.28
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.29
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.28
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.32
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.18
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.3
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.11
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.15
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 0.27
rrl 1474637 n.980C>G non_coding_transcript_exon_variant 0.18
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.27
rrl 1474643 n.986A>G non_coding_transcript_exon_variant 0.17
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.25
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.18
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.24
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.24
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.27
rrl 1474706 n.1049G>A non_coding_transcript_exon_variant 0.19
rrl 1474711 n.1054G>C non_coding_transcript_exon_variant 0.14
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 0.14
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 0.13
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.4
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.42
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.3
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.17
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.5
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.38
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.25
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.11
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.1
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.16
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.16
rrl 1475910 n.2253A>T non_coding_transcript_exon_variant 0.11
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.11
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.11
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.11
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.15
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.15
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.27
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.37
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.13
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.24
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 2169369 p.Gly415Ala 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 2715312 p.Ser7Arg missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_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 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 4243875 c.643C>T synonymous_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