TB-Profiler result

Run: SRR7535080
Summary

Run ID: SRR7535080

Sample name:

Date: 04-04-2023 19:44:25

Number of reads: 2435480

Percentage reads mapped: 9.78

Strain: lineage4.8

Drug-resistance: HR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
katG 2155692 p.Ser140Asn missense_variant 0.28 isoniazid
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 5078 c.-162_-161insG upstream_gene_variant 1.0
gyrB 6815 p.Lys526Gln missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576210 p.Ala288Asp missense_variant 0.12
rpoC 762894 c.-476C>T upstream_gene_variant 0.16
rpoB 762911 p.Ile1035Met missense_variant 0.38
rpoC 762923 c.-447C>G upstream_gene_variant 0.34
rpoC 762929 c.-441G>T upstream_gene_variant 0.35
rpoC 762932 c.-438G>T upstream_gene_variant 0.35
rpoB 762939 p.Met1045Leu missense_variant 0.32
rpoB 762942 p.Ile1046Val missense_variant 0.31
rpoC 762947 c.-423C>G upstream_gene_variant 0.33
rpoC 762962 c.-408C>T upstream_gene_variant 0.37
rpoC 762989 c.-381G>T upstream_gene_variant 0.36
rpoC 762998 c.-372G>A upstream_gene_variant 0.28
rpoC 764695 c.1326T>C synonymous_variant 0.13
rpoC 764705 c.1336C>T synonymous_variant 0.12
rpoC 764713 c.1344G>C synonymous_variant 0.13
rpoC 766628 c.3262dupG frameshift_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775855 p.Gly876Ser 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 1472153 n.308G>A non_coding_transcript_exon_variant 0.33
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.8
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.85
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.83
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.76
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.78
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.77
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.7
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.69
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.63
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.43
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.62
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.56
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.55
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.56
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.23
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.4
rrs 1472648 n.803G>C non_coding_transcript_exon_variant 0.2
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.75
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.75
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.81
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.77
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.71
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.7
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.67
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.52
rrs 1472824 n.979T>C non_coding_transcript_exon_variant 0.19
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.35
rrs 1472956 n.1111T>A non_coding_transcript_exon_variant 0.22
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.11
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.19
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.19
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.22
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.36
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.38
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.56
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.57
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.59
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.6
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.6
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.61
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.61
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.62
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.61
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.32
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.26
rrl 1474221 n.564T>C non_coding_transcript_exon_variant 0.25
rrl 1474228 n.571T>A non_coding_transcript_exon_variant 0.25
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.25
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.23
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.2
rrl 1475787 n.2130C>T non_coding_transcript_exon_variant 0.21
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.49
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.52
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.74
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.77
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.18
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.76
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.79
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.84
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.84
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.83
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.82
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.78
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.79
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.78
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.78
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.78
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.85
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.87
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.79
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.79
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.56
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.55
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.45
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.45
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.4
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.4
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.38
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.21
fabG1 1673312 c.-128C>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155668 c.444G>C synonymous_variant 0.24
katG 2155674 c.438G>C synonymous_variant 0.24
katG 2155691 c.421T>C synonymous_variant 0.28
katG 2155716 c.396T>C synonymous_variant 0.25
PPE35 2170049 c.564G>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859607 p.Arg271Leu missense_variant 0.11
pepQ 2859983 p.Ala146Ser missense_variant 0.11
thyA 3073806 c.666C>G synonymous_variant 0.17
alr 3840764 c.657G>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0