TB-Profiler result

Run: SRR12199400
Summary

Run ID: SRR12199400

Sample name:

Date: 03-04-2023 06:37:27

Number of reads: 135450

Percentage reads mapped: 20.01

Strain: lineage4.9;lineage1.1

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 0.94
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.32
lineage4.9 Euro-American (H37Rv-like) T1 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575664 p.Gly106Ala missense_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.5
mmpL5 776021 c.2460G>C synonymous_variant 0.5
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417038 p.Ser104Cys missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.5
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.15
rrs 1472128 n.283G>T non_coding_transcript_exon_variant 0.15
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.5
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.55
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.28
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.29
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.23
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.27
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.23
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.25
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.25
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.27
rrs 1472263 n.418C>T non_coding_transcript_exon_variant 0.27
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.27
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.29
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.44
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.43
rrs 1472405 n.560C>T non_coding_transcript_exon_variant 0.25
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.44
rrs 1472518 n.673G>A non_coding_transcript_exon_variant 0.36
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.35
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.56
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.47
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.36
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.34
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.39
rrs 1472581 n.736A>G non_coding_transcript_exon_variant 0.4
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.39
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.51
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.58
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.6
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.47
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.42
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.39
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.39
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.39
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.35
rrs 1472683 n.839_842delGGGA non_coding_transcript_exon_variant 0.37
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.35
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.33
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.3
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.32
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.37
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.51
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.53
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.46
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.38
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.29
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.2
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.19
rrs 1472839 n.994C>G non_coding_transcript_exon_variant 0.12
rrs 1472845 n.1000G>T non_coding_transcript_exon_variant 0.12
rrs 1472850 n.1005T>C non_coding_transcript_exon_variant 0.11
rrs 1472874 n.1029C>A non_coding_transcript_exon_variant 0.12
rrs 1472876 n.1031G>C non_coding_transcript_exon_variant 0.17
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.24
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.47
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.39
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.33
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.26
rrs 1473189 n.1344C>G non_coding_transcript_exon_variant 0.17
rrs 1473208 n.1363G>C non_coding_transcript_exon_variant 0.25
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.27
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.19
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.17
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.12
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.12
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.4
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.5
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.82
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.62
rrl 1474228 n.571T>A non_coding_transcript_exon_variant 0.68
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.44
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.45
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.5
rrl 1474869 n.1212G>C non_coding_transcript_exon_variant 0.33
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.43
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.43
rrl 1474902 n.1245T>G non_coding_transcript_exon_variant 0.22
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.22
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.22
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.29
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.38
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.18
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.48
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.48
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.47
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.5
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.61
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.66
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.53
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.21
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 0.29
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.29
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.45
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.52
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.65
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.71
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.76
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.72
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.72
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.72
rrl 1476420 n.2763G>A non_coding_transcript_exon_variant 0.74
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.76
rrl 1476433 n.2776C>T non_coding_transcript_exon_variant 0.71
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.6
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.53
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.55
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.45
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.39
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.3
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.36
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.31
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.29
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.29
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.29
rrl 1476528 n.2871A>T non_coding_transcript_exon_variant 0.3
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.29
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.31
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.31
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.31
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.32
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.49
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.57
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.45
rrl 1476595 n.2938C>A non_coding_transcript_exon_variant 0.22
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.22
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.22
rrl 1476601 n.2944G>A non_coding_transcript_exon_variant 0.22
rrl 1476602 n.2945G>T non_coding_transcript_exon_variant 0.22
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.22
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.22
rrl 1476621 n.2964C>A non_coding_transcript_exon_variant 0.24
rrl 1476628 n.2971T>C non_coding_transcript_exon_variant 0.24
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.24
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.24
rrl 1476637 n.2980C>A non_coding_transcript_exon_variant 0.24
rrl 1476645 n.2988A>G non_coding_transcript_exon_variant 0.25
rrl 1476657 n.3000G>T non_coding_transcript_exon_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 1.0
PPE35 2167967 c.2646A>C synonymous_variant 1.0
PPE35 2169369 p.Gly415Ala missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.8
PPE35 2170053 p.Thr187Ser missense_variant 0.8
PPE35 2170234 c.378delT frameshift_variant 0.5
pncA 2290199 c.-958C>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.86
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747294 p.Gln102Arg missense_variant 0.4
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.22
clpC1 4039645 p.His354Asp missense_variant 0.33
clpC1 4040517 p.Val63Ala missense_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244840 c.1608G>A synonymous_variant 1.0
embB 4247426 p.Gly305Thr missense_variant 0.33
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408341 c.-139G>T upstream_gene_variant 1.0