TB-Profiler result

Run: SRR7898217
Summary

Run ID: SRR7898217

Sample name:

Date: 15-08-2022 11:46:47

Number of reads: 2020961

Percentage reads mapped: 66.49

Strain: lineage1.1.2

Drug-resistance: MDR-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 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
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289054 p.Asp63Gly missense_variant 0.96 pyrazinamide
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 0.99
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 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.2
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.2
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.19
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.19
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.19
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.19
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.19
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.2
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.2
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.2
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.21
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.21
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.21
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.21
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.14
rrl 1473615 n.-43G>C upstream_gene_variant 1.0
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.16
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.15
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.15
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.15
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.22
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.22
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.22
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.24
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.15
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.25
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.25
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.24
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.24
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.24
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.24
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.16
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.15
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
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.18
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 0.98
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 0.98
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 4407869 p.Val112Phe missense_variant 0.97
gid 4407873 c.330G>T synonymous_variant 0.98
gid 4407985 p.Gly73Glu missense_variant 0.97