TB-Profiler result

Run: SRR1062869
Summary

Run ID: SRR1062869

Sample name:

Date: 02-04-2023 18:37:38

Number of reads: 196143

Percentage reads mapped: 3.96

Strain: lineage4.9

Drug-resistance: Pre-XDR-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
lineage4.9 Euro-American (H37Rv-like) T1 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155841 p.Trp91Arg missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326996 c.477delG frameshift_variant 1.0 ethionamide, ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7596 p.Met99Leu missense_variant 0.29
mshA 576066 p.Pro240His missense_variant 0.67
rpoC 764605 c.1236G>C synonymous_variant 0.5
rpoC 764611 c.1242G>C synonymous_variant 0.64
rpoC 764617 c.1248C>T synonymous_variant 0.78
rpoC 764623 c.1254C>G synonymous_variant 0.79
rpoC 764632 c.1263T>C synonymous_variant 0.86
rpoC 764647 c.1278C>T synonymous_variant 0.86
rpoC 764650 c.1281G>T synonymous_variant 0.86
rpoC 764658 c.1289_1290insTAC disruptive_inframe_insertion 0.85
rpoC 764662 c.1295_1297delTCG disruptive_inframe_deletion 0.85
rpoC 764671 c.1302G>A synonymous_variant 0.81
rpoC 764672 p.Gln435Thr missense_variant 0.81
rpoC 764918 p.Val517Met missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 0.3
rrs 1471877 n.32A>T non_coding_transcript_exon_variant 0.3
rrs 1471878 n.33C>T non_coding_transcript_exon_variant 0.3
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.36
rrs 1471898 n.53A>T non_coding_transcript_exon_variant 0.33
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.78
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.96
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.99
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.99
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.98
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.98
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.98
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.97
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.96
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.96
rrs 1472278 n.433C>T non_coding_transcript_exon_variant 0.71
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.44
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.4
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.79
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.67
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.62
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.57
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.25
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.96
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.97
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.95
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.95
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.95
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.95
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.95
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.95
rrs 1472824 n.979T>C non_coding_transcript_exon_variant 0.42
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.6
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.5
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.5
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.62
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.87
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.9
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.95
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.95
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.95
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.93
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.93
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.95
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.95
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.96
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.96
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.94
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.96
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.82
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.67
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.67
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.33
rrl 1475787 n.2130C>T non_coding_transcript_exon_variant 0.41
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.57
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.57
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.65
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.62
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.5
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.4
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.71
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.95
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.95
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.96
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.96
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.96
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.96
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.96
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.96
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.96
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.96
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.97
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.98
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.98
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.98
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.96
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.97
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.97
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.97
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.98
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.98
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.95
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.95
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.95
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.92
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.6
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.6
PPE35 2169331 p.Asn428Tyr missense_variant 0.4
PPE35 2169570 p.Ser348Ile missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288889 p.Asn118Ser missense_variant 1.0
pncA 2289138 p.Leu35Arg missense_variant 1.0
fbiD 3339385 p.Asp90Asn missense_variant 1.0
panD 4044432 c.-151T>A upstream_gene_variant 0.33
ubiA 4269783 c.50delT frameshift_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0