TB-Profiler result

Run: SRR11349174
Summary

Run ID: SRR11349174

Sample name:

Date: 02-04-2023 20:54:32

Number of reads: 4651615

Percentage reads mapped: 66.83

Strain: lineage4.4.1.1.1

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 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 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 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289069 p.Phe58Ser missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala 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 5239 c.-1C>G upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575719 c.372C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.36
rpoC 764944 p.His525Gln missense_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.12
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.1
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.15
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.1
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.11
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.12
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.28
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.27
rrs 1472972 n.1127T>A non_coding_transcript_exon_variant 0.23
rrs 1472974 n.1130_1133delTGGT non_coding_transcript_exon_variant 0.24
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.21
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.24
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.24
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 0.2
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.21
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.18
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.15
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.18
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.13
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.24
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.37
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.41
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.31
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.43
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.31
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.31
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.33
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.29
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.39
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.14
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.26
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.29
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.29
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.25
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.3
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.23
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.13
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.19
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
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
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.19
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
rpoA 3878641 c.-134C>G upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0