TB-Profiler result

Run: SRR9971243
Summary

Run ID: SRR9971243

Sample name:

Date: 04-04-2023 23:18:43

Number of reads: 5634778

Percentage reads mapped: 94.36

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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.Asp435Gly missense_variant 1.0 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288785 c.456dupC frameshift_variant 0.99 pyrazinamide, pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.75 para-aminosalicylic_acid
ald 3087656 c.839_843dupCGACC frameshift_variant 0.98 cycloserine
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
thyA 3072874 c.-601_*805del transcript_ablation 1.0 para-aminosalicylic_acid
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
rpoB 763123 p.Ile1106Thr missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.54
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.65
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.68
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.68
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.71
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.68
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.74
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.77
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.8
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.8
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.8
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.79
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.71
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.69
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.69
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.22
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.29
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.29
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.29
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.57
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.57
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.57
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.57
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.57
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.75
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.88
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.88
rrs 1472579 n.734G>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 0.77
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.87
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.82
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.78
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.78
rrs 1472669 n.824_825insTGG non_coding_transcript_exon_variant 0.69
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.6
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.6
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.6
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.64
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.71
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.69
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.75
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.81
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.81
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.81
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.81
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.81
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.55
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.44
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.3
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.38
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.43
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.43
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.43
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.38
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.38
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.38
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.38
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.38
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.33
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.33
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.33
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.33
rrs 1473002 n.1157G>C non_coding_transcript_exon_variant 0.33
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.33
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.33
rrs 1473009 n.1164T>A non_coding_transcript_exon_variant 0.33
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.3
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.2
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.2
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.18
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.2
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.3
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.25
rrl 1473862 n.205C>A non_coding_transcript_exon_variant 0.43
rrl 1473867 n.210C>G non_coding_transcript_exon_variant 0.38
rrl 1473871 n.214T>G non_coding_transcript_exon_variant 0.38
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.38
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.38
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.38
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.43
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.5
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.4
rrl 1474249 n.592G>C non_coding_transcript_exon_variant 0.5
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.5
rrl 1474816 n.1159G>C non_coding_transcript_exon_variant 0.5
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.67
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.5
rrl 1474830 n.1173A>C non_coding_transcript_exon_variant 0.5
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.5
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.67
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.83
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.71
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.2
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.25
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.29
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.29
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.29
rrl 1475819 n.2162C>T non_coding_transcript_exon_variant 0.12
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.13
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.44
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.67
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.71
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.74
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.76
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.76
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.76
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.81
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.81
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.81
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.81
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.81
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.81
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.82
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.84
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.86
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.9
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.94
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.96
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.91
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.91
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 1.0
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.91
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.83
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.83
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.83
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.77
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.77
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.77
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.89
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.9
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.9
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.9
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.91
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.92
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.92
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.93
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.93
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.95
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.98
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.97
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 1.0
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 1.0
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 1.0
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.82
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.9
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.9
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.9
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.9
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.82
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.82
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.8
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.75
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.7
rrl 1476595 n.2938C>A non_coding_transcript_exon_variant 0.29
rrl 1476602 n.2945G>T non_coding_transcript_exon_variant 0.25
inhA 1673692 c.-510C>G upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221848 c.1317A>G synonymous_variant 1.0
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyX 3067949 c.-4C>T upstream_gene_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642408 p.Thr292Ala missense_variant 1.0
alr 3841405 p.Glu6Gln missense_variant 0.96
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269271 p.Val188Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407922 p.Leu94Gln missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0