TB-Profiler result

Run: SRR13861596
Summary

Run ID: SRR13861596

Sample name:

Date: 03-04-2023 09:35:53

Number of reads: 1428964

Percentage reads mapped: 28.61

Strain: lineage4.9

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 0.98
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
rrs 1472122 n.277G>C non_coding_transcript_exon_variant 0.86 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
gyrB 5319 p.Arg27Leu missense_variant 0.97
rpoB 760867 p.Gly354Asp missense_variant 0.95
rpoC 762443 c.-927G>C upstream_gene_variant 0.14
rpoC 762470 c.-900G>C upstream_gene_variant 0.15
rpoB 762489 p.Val895Gln missense_variant 0.16
rpoB 762496 c.2691delC frameshift_variant 0.86
rpoC 764405 c.1036A>C synonymous_variant 0.14
rpoC 764434 c.1065A>G synonymous_variant 0.17
rpoC 764446 c.1077T>C synonymous_variant 0.2
rpoC 764793 p.Met475Arg missense_variant 0.94
rpoC 764893 c.1524T>C synonymous_variant 0.17
rpoC 764911 c.1542A>G synonymous_variant 0.16
rpoC 764923 c.1554A>G synonymous_variant 0.16
rpoC 764932 c.1563C>A synonymous_variant 0.15
rpoC 764968 c.1599T>C synonymous_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.15
rpoC 765007 c.1638T>G synonymous_variant 0.13
rpoC 765019 c.1650A>G synonymous_variant 0.14
rpoC 765022 c.1653G>C synonymous_variant 0.14
rpoC 765796 c.2427C>T synonymous_variant 0.15
rpoC 765811 c.2442T>C synonymous_variant 0.17
rpoC 765814 c.2445A>G synonymous_variant 0.16
rpoC 766408 c.3039C>T synonymous_variant 0.13
rpoC 766426 c.3057C>T synonymous_variant 0.16
rpoC 766447 c.3078T>C synonymous_variant 0.16
rpoC 766483 c.3114G>C synonymous_variant 0.18
rpoC 766484 p.Val1039Ile missense_variant 0.17
rpoC 766492 c.3123T>C synonymous_variant 0.18
rpoC 766495 c.3126C>T synonymous_variant 0.19
rpoC 766522 c.3153C>G synonymous_variant 0.18
rpoC 766528 c.3159T>C synonymous_variant 0.17
rpoC 766531 c.3162G>T synonymous_variant 0.17
rpoC 766549 c.3180G>C synonymous_variant 0.15
rpoC 766563 p.Thr1065Ser missense_variant 0.85
rpoC 766933 c.3564A>G synonymous_variant 0.14
rpoC 766945 c.3576A>G synonymous_variant 0.19
rpoC 766963 c.3594T>C synonymous_variant 0.14
rpoC 766978 c.3609C>G synonymous_variant 0.14
rpoC 766996 c.3627C>T synonymous_variant 0.17
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.17
rpoC 767014 c.3645G>C synonymous_variant 0.17
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.17
rpoC 767059 c.3690T>G synonymous_variant 0.17
rpoC 767062 c.3693C>A synonymous_variant 0.19
rpoC 767074 c.3705T>C synonymous_variant 0.17
rpoC 767098 c.3729T>C synonymous_variant 0.13
rpoC 767119 c.3750A>G synonymous_variant 0.15
rpoC 767167 c.3798C>G synonymous_variant 0.13
mmpL5 775976 c.2505G>C synonymous_variant 0.95
mmpL5 776814 p.Gln556Arg missense_variant 1.0
rplC 800623 c.-186A>C upstream_gene_variant 0.91
rplC 800769 c.-40A>T upstream_gene_variant 0.91
fbiC 1302878 c.-53C>G upstream_gene_variant 1.0
fbiC 1303535 p.Ser202Leu missense_variant 1.0
atpE 1461256 p.Met71Arg missense_variant 0.96
rrs 1471836 n.-10A>G upstream_gene_variant 1.0
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.15
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.12
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.13
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.14
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.15
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.37
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.5
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.5
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.5
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.55
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.53
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.53
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.53
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.53
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.53
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.51
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.52
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.53
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.52
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.53
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.49
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.5
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
katG 2156157 c.-46C>A upstream_gene_variant 1.0
PPE35 2168627 p.Ile662Met missense_variant 1.0
Rv1979c 2222100 c.1065T>A synonymous_variant 1.0
pncA 2289242 c.-1T>C upstream_gene_variant 1.0
ribD 2987205 p.Ser123Ala missense_variant 1.0
ribD 2987347 p.Pro170Leu missense_variant 1.0
Rv3083 3448903 p.Asp134His missense_variant 1.0
rpoA 3877656 c.852T>C synonymous_variant 0.16
rpoA 3877743 c.765T>C synonymous_variant 0.13
rpoA 3877770 c.738A>G synonymous_variant 0.14
rpoA 3877776 c.732T>C synonymous_variant 0.14
rpoA 3878376 c.132G>C synonymous_variant 0.14
rpoA 3878385 c.123C>G synonymous_variant 0.14
rpoA 3878391 c.117T>C synonymous_variant 0.14
rpoA 3878396 c.112C>T synonymous_variant 0.14
clpC1 4039663 p.Gly348Ser missense_variant 0.96
embC 4240726 c.864G>C synonymous_variant 0.13
embC 4241256 p.Arg465Thr missense_variant 1.0
embA 4245137 c.1905T>C synonymous_variant 0.13
embA 4245149 c.1917C>G synonymous_variant 0.13
embA 4246449 p.Val1073Phe missense_variant 1.0
embB 4248035 p.Val508Ile missense_variant 0.13
embB 4248041 p.Ala510Thr missense_variant 0.15
embB 4248055 c.1542G>C synonymous_variant 0.14
embB 4248064 c.1551G>C synonymous_variant 0.14
embB 4248097 c.1584C>G synonymous_variant 0.16
embB 4248127 c.1614G>C synonymous_variant 0.13
embB 4248133 c.1620C>G synonymous_variant 0.18
embB 4248142 c.1629T>C synonymous_variant 0.15
embB 4248143 c.1630T>C synonymous_variant 0.15
embB 4248157 c.1644A>G synonymous_variant 0.19
embB 4248206 p.Ser565Gly missense_variant 0.15
embB 4248220 c.1707A>G synonymous_variant 0.14
embB 4248265 c.1752C>T synonymous_variant 0.13
aftB 4268192 c.645G>C synonymous_variant 1.0