TB-Profiler result

Run: SRR1062897
Summary

Run ID: SRR1062897

Sample name:

Date: 02-04-2023 18:39:17

Number of reads: 1840410

Percentage reads mapped: 69.37

Strain: lineage4.4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 0.99
lineage4.4.1.1 Euro-American S;Orphans None 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
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 5195 c.-45C>G upstream_gene_variant 0.94
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762899 c.-471G>C upstream_gene_variant 0.12
rpoC 762917 c.-453C>G upstream_gene_variant 0.1
rpoC 762923 c.-447C>G upstream_gene_variant 0.12
rpoB 762925 p.Thr1040Ile missense_variant 0.12
rpoC 764581 c.1212T>C synonymous_variant 0.1
rpoC 764582 p.Leu405Met missense_variant 0.12
rpoC 764587 c.1218C>G synonymous_variant 0.12
rpoC 764605 c.1236G>C synonymous_variant 0.17
rpoC 764611 c.1242G>T synonymous_variant 0.2
rpoC 764632 c.1263T>C synonymous_variant 0.2
rpoC 764641 c.1272C>T synonymous_variant 0.19
rpoC 764650 c.1281G>T synonymous_variant 0.19
rpoC 764663 p.Val432Thr missense_variant 0.16
rpoC 764672 p.Gln435Glu missense_variant 0.14
rpoC 764677 c.1308C>G synonymous_variant 0.12
rpoC 764695 c.1326T>C synonymous_variant 0.1
rpoC 766641 p.His1091Arg missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.16
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.15
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.17
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.14
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.15
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.15
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.14
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.14
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.19
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.18
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.18
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.39
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.45
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.4
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.43
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.26
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.27
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.2
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.16
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.29
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.28
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.24
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.25
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.11
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.13
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.26
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.26
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.26
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.32
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.31
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.37
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.38
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.49
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.49
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.52
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.47
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.48
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.46
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.46
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.4
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.35
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.16
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746923 p.Gly226Ser missense_variant 1.0
pepQ 2860173 c.246C>T synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243692 p.Gly154Ser missense_variant 1.0
embB 4246904 p.Val131Met missense_variant 0.97
ethA 4328252 c.-779T>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407758 p.Ser149Arg missense_variant 1.0