TB-Profiler result

Run: SRR1196557
Summary

Run ID: SRR1196557

Sample name:

Date: 03-04-2023 05:28:50

Number of reads: 83439

Percentage reads mapped: 3.49

Strain: lineage4.9;lineage2.2

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
lineage2 East-Asian Beijing RD105 0.05
lineage4 Euro-American LAM;T;S;X;H None 0.95
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.09
lineage4.9 Euro-American (H37Rv-like) T1 None 0.96
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 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.95 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 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 7030 c.1792_1794delGGG conservative_inframe_deletion 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776332 c.2149C>A synonymous_variant 0.5
mmpL5 776362 p.Gln707* stop_gained 0.4
mmpL5 776384 c.2097C>T synonymous_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 0.75
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.67
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.67
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.67
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.67
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.8
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 1.0
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 1.0
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.83
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.83
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.83
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.6
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
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 0.98
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.98
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.98
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.71
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.6
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.92
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.96
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.97
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.96
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.96
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.94
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.93
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.9
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.67
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.5
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.5
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.43
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.43
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.29
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.43
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.5
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.6
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.6
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.6
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.6
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.75
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.6
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.5
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.5
rrl 1475574 n.1917C>A non_coding_transcript_exon_variant 0.67
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.83
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.75
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.75
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.75
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.75
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.83
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.83
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.92
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.93
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.95
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.96
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.97
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.95
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.96
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.99
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.99
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.99
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.89
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.83
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.6
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.5
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.5
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.5
katG 2156218 c.-107G>T upstream_gene_variant 0.29
PPE35 2168311 p.Gln768* stop_gained 1.0
PPE35 2169914 c.699C>A synonymous_variant 0.67
PPE35 2169919 p.Leu232Ile missense_variant 0.67
Rv1979c 2222136 p.Lys343Asn missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.33
folC 2747142 p.Glu153* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242999 p.Ala1046Val missense_variant 0.67
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245287 c.2055G>A synonymous_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 1.0