TB-Profiler result

Run: SRR10315715
Summary

Run ID: SRR10315715

Sample name:

Date: 02-04-2023 17:17:18

Number of reads: 8315835

Percentage reads mapped: 93.45

Strain: lineage4.4.1.1.1

Drug-resistance: MDR-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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 Euro-American S;Orphans 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.56 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289069 p.Phe58Ser missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
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 5239 c.-1C>G upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575719 c.372C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.34
mshA 576485 p.Ala380Ser missense_variant 0.15
rpoC 764944 p.His525Gln missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.3
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.25
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.38
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.3
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.27
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.25
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.25
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.13
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.25
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.22
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.24
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.44
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.24
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.24
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.16
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.32
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.33
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.3
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.3
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.24
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.25
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.22
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.25
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.25
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.24
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.21
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.32
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.26
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.41
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.47
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.59
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.61
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.47
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.54
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.42
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.13
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.14
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.15
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.15
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.16
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.12
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.18
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.18
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.21
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.12
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.17
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.24
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.17
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.18
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.15
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.16
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.15
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.13
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.13
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.18
rrl 1474199 n.542G>A non_coding_transcript_exon_variant 0.18
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.2
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.12
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.12
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.23
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.25
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.25
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.25
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.25
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.25
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.27
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.27
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.25
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.25
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.24
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.24
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.15
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.13
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.1
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.1
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.12
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.11
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.12
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.12
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.12
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.12
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.12
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.12
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.18
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.18
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.31
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.35
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.31
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.34
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.32
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.32
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.13
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.24
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.32
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.22
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.1
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.12
Rv3083 3448608 c.105G>A synonymous_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0