TB-Profiler result

Run: SRR1184379
Summary

Run ID: SRR1184379

Sample name:

Date: 03-04-2023 05:20:58

Number of reads: 133289

Percentage reads mapped: 6.41

Strain: lineage4

Drug-resistance: Other

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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 0.95
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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.67 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.91 streptomycin
alr 3841083 p.Leu113Arg missense_variant 0.67 cycloserine
embB 4247431 p.Met306Ile missense_variant 0.67 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.75
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763582 p.Lys71Asn missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775753 p.Ile910Val missense_variant 0.4
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776176 c.2304delG frameshift_variant 0.4
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302957 c.27C>T synonymous_variant 0.4
fbiC 1305455 p.Arg842His missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472070 n.225G>T non_coding_transcript_exon_variant 0.33
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.43
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.43
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.43
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.43
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.56
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.56
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.56
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.56
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.62
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.86
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.93
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.96
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.96
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.98
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.98
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.98
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.98
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.99
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.99
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.99
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.99
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.99
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.97
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.76
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.6
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.81
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.93
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.92
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.92
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.92
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.91
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.89
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.86
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.68
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.53
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.53
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.78
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.64
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.6
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.6
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.64
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.5
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.45
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.58
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.55
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.55
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.6
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.67
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.73
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.73
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.73
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.79
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.8
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.8
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.86
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.5
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.5
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.5
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.4
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.4
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.4
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.71
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.79
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.79
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.73
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.75
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.62
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.62
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.38
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.2
rrl 1476126 n.2469C>T non_coding_transcript_exon_variant 0.5
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.6
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.6
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.6
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.57
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.6
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.29
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.6
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.6
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.62
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.93
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.92
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.96
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.97
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.98
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.98
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.98
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.98
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.96
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.97
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.97
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.91
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.86
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.81
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.71
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.67
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.67
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.57
rpsA 1834177 c.636A>C synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169714 p.Gly300Val missense_variant 0.22
PPE35 2169896 c.717C>T synonymous_variant 0.18
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726191 c.-2T>A upstream_gene_variant 0.67
folC 2746248 p.Ala451Thr missense_variant 0.67
ribD 2987175 p.Glu113* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840402 p.Arg340Leu missense_variant 0.29
embB 4248442 c.1929C>T synonymous_variant 0.33
aftB 4268258 c.579C>T synonymous_variant 0.4
ethA 4326517 c.957G>A synonymous_variant 0.4
ethA 4326692 p.Arg261Gln missense_variant 1.0
ethA 4328301 c.-828C>T upstream_gene_variant 0.25
gid 4407927 p.Glu92Asp missense_variant 1.0