TB-Profiler result

Run: SRR13861666
Summary

Run ID: SRR13861666

Sample name:

Date: 03-04-2023 09:37:36

Number of reads: 592974

Percentage reads mapped: 59.35

Strain: lineage4.9

Drug-resistance: Sensitive

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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
lineage4.9 Euro-American (H37Rv-like) T1 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
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 5149 c.-91G>C upstream_gene_variant 1.0
gyrA 6362 c.-940T>C upstream_gene_variant 0.12
gyrB 7090 p.Asp617Glu missense_variant 0.92
gyrA 7099 c.-203G>A upstream_gene_variant 0.17
gyrA 7108 c.-194G>A upstream_gene_variant 0.15
gyrA 7114 c.-188C>A upstream_gene_variant 0.15
gyrB 7124 p.Ser629Thr missense_variant 0.15
gyrA 7129 c.-173T>G upstream_gene_variant 0.15
gyrA 7132 c.-170T>G upstream_gene_variant 0.15
gyrA 7136 c.-166T>C upstream_gene_variant 0.15
gyrA 7141 c.-161T>C upstream_gene_variant 0.15
gyrA 7144 c.-158A>G upstream_gene_variant 0.15
gyrA 7147 c.-155G>C upstream_gene_variant 0.14
gyrA 8436 p.Tyr379Asn missense_variant 0.96
gyrA 8996 c.1695T>C synonymous_variant 0.12
fgd1 491701 p.His307Asn missense_variant 1.0
ccsA 619765 c.-126G>A upstream_gene_variant 1.0
rpoB 762167 c.2361T>C synonymous_variant 0.13
rpoB 762176 c.2370T>C synonymous_variant 0.17
rpoB 762185 c.2379G>C synonymous_variant 0.19
rpoB 762218 c.2412T>G synonymous_variant 0.19
rpoB 762254 c.2448T>C synonymous_variant 0.17
rpoB 762266 c.2460T>C synonymous_variant 0.19
rpoB 762284 c.2478G>C synonymous_variant 0.19
rpoB 762293 c.2487T>C synonymous_variant 0.13
rpoB 762317 c.2511A>G synonymous_variant 0.19
rpoB 762329 c.2523G>C synonymous_variant 0.2
rpoB 762338 c.2532T>C synonymous_variant 0.2
rpoB 762347 c.2541T>C synonymous_variant 0.15
rpoB 762362 p.Glu852Asp missense_variant 0.21
rpoB 762369 c.2563T>C synonymous_variant 0.21
rpoC 762374 c.-996G>C upstream_gene_variant 0.21
rpoC 762380 c.-990T>G upstream_gene_variant 0.21
rpoC 762395 c.-975G>C upstream_gene_variant 0.2
rpoC 762398 c.-972T>C upstream_gene_variant 0.2
rpoC 762401 c.-969G>C upstream_gene_variant 0.18
rpoC 762404 c.-966T>C upstream_gene_variant 0.18
rpoC 762410 c.-960T>C upstream_gene_variant 0.18
rpoC 762416 c.-954A>G upstream_gene_variant 0.18
rpoC 762443 c.-927G>C upstream_gene_variant 0.16
rpoC 763202 c.-168A>C upstream_gene_variant 0.12
rpoC 763214 c.-156T>C upstream_gene_variant 0.13
rpoC 763220 c.-150G>C upstream_gene_variant 0.12
rpoC 764893 c.1524T>C synonymous_variant 0.13
rpoC 764911 c.1542A>G synonymous_variant 0.16
rpoC 766630 c.3261G>C synonymous_variant 0.2
rpoC 766645 c.3276A>G synonymous_variant 0.13
rpoC 766651 c.3282T>C synonymous_variant 0.12
rpoC 766657 c.3288A>G synonymous_variant 0.12
rpoC 766672 c.3303T>C synonymous_variant 0.14
rpoC 766738 c.3369G>T synonymous_variant 0.17
rpoC 766750 c.3381C>G synonymous_variant 0.18
rpoC 766765 c.3396A>C synonymous_variant 0.12
rpoC 766774 c.3405T>C synonymous_variant 0.12
mmpL5 775867 p.Arg872Gly missense_variant 1.0
mmpL5 776710 p.Cys591Ser missense_variant 1.0
mmpL5 777625 p.Gln286Lys missense_variant 1.0
mmpS5 778811 p.Phe32Ser missense_variant 1.0
rpsL 781859 c.300T>C synonymous_variant 0.12
rpsL 781868 c.309T>C synonymous_variant 0.13
rpsL 781871 c.312G>C synonymous_variant 0.14
rpsL 781892 c.333A>G synonymous_variant 0.15
rpsL 781898 c.339A>T synonymous_variant 0.15
rpsL 781916 c.357T>C synonymous_variant 0.13
rpsL 781929 p.Gly124Ser missense_variant 0.13
fbiC 1303464 c.534A>T synonymous_variant 0.15
embR 1416901 c.447G>C synonymous_variant 1.0
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.11
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.11
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.12
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.12
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.12
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.13
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.13
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.12
rrl 1473945 n.288T>C non_coding_transcript_exon_variant 0.12
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.14
rrl 1474466 n.810delA non_coding_transcript_exon_variant 1.0
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.12
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.12
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.12
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.12
rrl 1475224 n.1567T>C non_coding_transcript_exon_variant 0.88
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.16
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.12
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.12
rrl 1475271 n.1614A>C non_coding_transcript_exon_variant 0.13
rrl 1475273 n.1616T>A non_coding_transcript_exon_variant 0.14
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.15
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.15
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.18
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.18
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.18
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.15
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.14
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.14
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.16
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.16
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.16
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.16
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.17
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.15
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.15
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.15
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.16
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.19
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.17
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.17
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.17
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.16
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.15
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.15
rrl 1476589 n.2932G>A non_coding_transcript_exon_variant 1.0
inhA 1673607 c.-595T>C upstream_gene_variant 0.12
inhA 1673610 c.-592C>T upstream_gene_variant 0.14
inhA 1673616 c.-586A>G upstream_gene_variant 0.13
inhA 1673619 c.-583T>C upstream_gene_variant 0.13
fabG1 1673633 p.Ser65Asn missense_variant 0.15
inhA 1673646 c.-556T>C upstream_gene_variant 0.17
inhA 1673658 c.-544G>A upstream_gene_variant 0.14
inhA 1673660 c.-542C>A upstream_gene_variant 0.14
inhA 1673664 c.-538A>G upstream_gene_variant 0.13
inhA 1673667 c.-535A>G upstream_gene_variant 0.13
inhA 1673679 c.-523T>G upstream_gene_variant 0.13
inhA 1674624 c.423A>C synonymous_variant 0.12
inhA 1674627 c.426T>G synonymous_variant 0.13
inhA 1674630 c.429C>G synonymous_variant 0.14
inhA 1674636 c.435C>G synonymous_variant 0.14
inhA 1674654 c.453G>C synonymous_variant 0.13
inhA 1674774 c.573A>G synonymous_variant 0.18
inhA 1674836 p.Gly212Ala missense_variant 0.17
inhA 1674876 c.675C>G synonymous_variant 0.12
rpsA 1833661 c.120A>G synonymous_variant 0.14
rpsA 1833667 c.126C>G synonymous_variant 0.14
rpsA 1833847 c.306C>G synonymous_variant 0.16
rpsA 1833856 c.315A>G synonymous_variant 0.17
rpsA 1833862 c.321G>T synonymous_variant 0.15
rpsA 1833874 c.333T>C synonymous_variant 0.14
rpsA 1833928 c.387G>C synonymous_variant 0.2
rpsA 1833940 c.399C>G synonymous_variant 0.16
rpsA 1833970 c.429G>C synonymous_variant 0.19
rpsA 1833979 c.438T>C synonymous_variant 0.18
rpsA 1834000 c.459G>C synonymous_variant 0.12
rpsA 1834015 c.474G>C synonymous_variant 0.12
rpsA 1834021 c.480C>T synonymous_variant 0.13
rpsA 1834348 c.807T>C synonymous_variant 0.13
rpsA 1834606 c.1065C>G synonymous_variant 0.11
rpsA 1834688 c.1147_1149delAGTinsTCC synonymous_variant 0.12
PPE35 2170487 c.126T>A synonymous_variant 0.94
Rv1979c 2221853 p.Phe438Ile missense_variant 1.0
ahpC 2726591 c.399C>G synonymous_variant 0.13
ahpC 2726593 p.Val134Ala missense_variant 0.13
folC 2747691 c.-93A>G upstream_gene_variant 0.2
folC 2747700 c.-102T>C upstream_gene_variant 0.18
folC 2747707 c.-109C>A upstream_gene_variant 0.17
folC 2747717 c.-119T>C upstream_gene_variant 0.14
folC 2747718 c.-120G>A upstream_gene_variant 0.14
folC 2747726 c.-128G>A upstream_gene_variant 0.15
folC 2747745 c.-147A>C upstream_gene_variant 0.15
folC 2747752 c.-154G>C upstream_gene_variant 0.18
folC 2747759 c.-161T>C upstream_gene_variant 0.18
folC 2747760 c.-162G>T upstream_gene_variant 0.18
folC 2747772 c.-174C>G upstream_gene_variant 0.17
folC 2747778 c.-180T>G upstream_gene_variant 0.14
folC 2747790 c.-192G>C upstream_gene_variant 0.15
ribD 2987369 c.531G>A synonymous_variant 1.0
thyA 3073975 p.Arg166Pro missense_variant 0.88
thyA 3073977 c.495A>G synonymous_variant 0.12
thyA 3073989 c.483T>C synonymous_variant 0.14
thyA 3074001 c.471C>G synonymous_variant 0.14
thyA 3074004 c.468T>C synonymous_variant 0.14
thyA 3074010 c.462C>G synonymous_variant 0.13
thyA 3074031 c.441T>C synonymous_variant 0.13
thyA 3074037 c.435C>G synonymous_variant 0.12
thyA 3074076 c.396C>G synonymous_variant 0.15
thyA 3074165 p.Ala103Thr missense_variant 0.12
thyA 3074175 c.297A>G synonymous_variant 0.14
thyA 3074181 c.291A>G synonymous_variant 0.13
thyA 3074184 c.288A>G synonymous_variant 0.13
thyA 3074187 c.285T>C synonymous_variant 0.12
thyA 3074199 c.273G>A synonymous_variant 0.12
Rv3236c 3612013 c.1104A>T synonymous_variant 1.0
Rv3236c 3612032 p.Met362Arg missense_variant 1.0
clpC1 4038498 p.Ser736Thr missense_variant 0.12
clpC1 4039334 c.1371G>C synonymous_variant 0.12
clpC1 4039338 p.Thr456Lys missense_variant 0.12
clpC1 4039388 c.1317C>A synonymous_variant 0.12
clpC1 4039391 c.1314T>G synonymous_variant 0.12
clpC1 4039517 c.1188C>G synonymous_variant 0.14
clpC1 4039524 p.Phe394Tyr missense_variant 0.19
clpC1 4039526 c.1179G>C synonymous_variant 0.19
clpC1 4039547 c.1158C>G synonymous_variant 0.17
clpC1 4039553 c.1152C>G synonymous_variant 0.17
clpC1 4039562 c.1143C>G synonymous_variant 0.19
clpC1 4039565 c.1140G>C synonymous_variant 0.19
clpC1 4039576 p.Ala377Ser missense_variant 0.2
clpC1 4039577 c.1128T>C synonymous_variant 0.2
clpC1 4039586 c.1119G>C synonymous_variant 0.18
clpC1 4039610 c.1095G>C synonymous_variant 0.2
clpC1 4039616 c.1089G>C synonymous_variant 0.21
clpC1 4039622 c.1083C>G synonymous_variant 0.17
clpC1 4039817 c.888A>T synonymous_variant 0.12
embC 4240425 p.Arg188Pro missense_variant 1.0
embC 4240477 c.615C>A synonymous_variant 1.0
embC 4240514 p.Val218Met missense_variant 0.12
embC 4240519 c.657T>C synonymous_variant 0.12
embC 4240819 c.957A>G synonymous_variant 0.15
embC 4240825 c.963G>A synonymous_variant 0.17
embC 4240831 c.969T>G synonymous_variant 0.16
embC 4240867 c.1005T>G synonymous_variant 0.17
embC 4240870 c.1008T>C synonymous_variant 0.16
embC 4240879 c.1017G>C synonymous_variant 0.16
embC 4240880 p.Ala340Thr missense_variant 0.15
embC 4240897 c.1035C>G synonymous_variant 0.15
embC 4240900 c.1038A>G synonymous_variant 0.15
embC 4240919 c.1057_1059delCTCinsTTG synonymous_variant 0.13
embC 4240936 c.1074A>G synonymous_variant 0.17
embC 4240945 c.1083T>C synonymous_variant 0.19
embC 4240951 c.1089C>G synonymous_variant 0.16
embC 4240954 p.Ile364Met missense_variant 0.21
embC 4240957 c.1095C>G synonymous_variant 0.17
embC 4240966 c.1104G>T synonymous_variant 0.12
embC 4241137 c.1275G>C synonymous_variant 0.13
embC 4241140 c.1278A>G synonymous_variant 0.12
embA 4244214 p.Ala328Ser missense_variant 1.0
embA 4244849 c.1617C>G synonymous_variant 1.0
embB 4247198 p.Thr229Pro missense_variant 1.0
embB 4247381 p.Trp290Arg missense_variant 0.95
embB 4248118 c.1605T>C synonymous_variant 0.13
embB 4248127 c.1614G>C synonymous_variant 0.13
embB 4248133 c.1620C>G synonymous_variant 0.12
embB 4248143 c.1630T>C synonymous_variant 0.12
aftB 4268115 p.Leu241Arg missense_variant 1.0
aftB 4268696 c.141G>A synonymous_variant 1.0
ethA 4326298 c.1176G>A synonymous_variant 1.0
whiB6 4338567 c.-46C>A upstream_gene_variant 1.0