TB-Profiler result

Run: SRR2101087
Summary

Run ID: SRR2101087

Sample name:

Date: 03-04-2023 23:29:57

Number of reads: 5068065

Percentage reads mapped: 85.23

Strain: lineage4.4.2

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 1.0
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.44 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.4 streptomycin
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.14
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.26
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.38
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.45
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.45
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.47
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.47
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.5
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.49
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.49
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.52
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.49
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.45
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.44
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.43
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.37
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.37
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.14
rrs 1472955 n.1110C>G non_coding_transcript_exon_variant 0.14
rrs 1472956 n.1111T>A non_coding_transcript_exon_variant 0.14
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.14
rrs 1472970 n.1125C>T non_coding_transcript_exon_variant 0.14
rrs 1472971 n.1126G>T non_coding_transcript_exon_variant 0.14
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.13
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.13
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.14
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.14
rrs 1472990 n.1145A>T non_coding_transcript_exon_variant 0.13
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.13
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.12
rrl 1475704 n.2047C>T non_coding_transcript_exon_variant 0.15
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.23
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.24
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.26
rrl 1475752 n.2095C>G non_coding_transcript_exon_variant 0.26
rrl 1475753 n.2096C>A non_coding_transcript_exon_variant 0.26
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.26
rrl 1475775 n.2118G>C non_coding_transcript_exon_variant 0.24
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.24
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.22
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.22
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.22
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.22
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.22
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.13
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.11
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.12
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.15
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.22
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.24
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.25
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.19
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.19
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.19
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.19
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.19
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.19
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.19
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.21
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.21
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.21
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.33
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.4
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.45
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.44
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.52
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.45
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.45
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.4
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.39
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.42
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.38
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.39
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.22
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.19
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.16
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.16
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.16
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.16
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.16
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.16
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.16
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.15
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.17
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.16
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.15
rrl 1476574 n.2917A>T non_coding_transcript_exon_variant 0.15
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.15
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.15
rrl 1476594 n.2937C>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087648 p.Gly277Ser missense_variant 1.0
Rv3083 3448348 c.-156G>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.99
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0