TB-Profiler result

Run: SRR13861168
Summary

Run ID: SRR13861168

Sample name:

Date: 03-04-2023 09:25:06

Number of reads: 1215768

Percentage reads mapped: 40.56

Strain: lineage4.9

Drug-resistance: RR-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
lineage4.9 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
rpoB 761135 p.Leu443Phe missense_variant 0.17 rifampicin
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 6286 c.1047T>C synonymous_variant 0.15
gyrA 7664 c.363T>C synonymous_variant 0.15
gyrA 7710 c.409T>C synonymous_variant 0.15
gyrA 7715 c.414G>C synonymous_variant 0.15
gyrA 7728 c.427_429delAGGinsCGC synonymous_variant 0.16
gyrA 7760 c.459C>T synonymous_variant 0.16
gyrA 7763 c.462T>C synonymous_variant 0.16
gyrA 8090 c.789C>G synonymous_variant 0.13
gyrA 8096 c.795T>C synonymous_variant 0.12
gyrA 8177 c.876A>C synonymous_variant 0.15
gyrA 8198 c.897T>C synonymous_variant 0.15
gyrA 8204 c.903C>T synonymous_variant 0.14
gyrA 8207 c.906T>C synonymous_variant 0.15
gyrA 8225 c.924T>C synonymous_variant 0.15
gyrA 8234 c.933T>G synonymous_variant 0.15
gyrA 8235 c.934_936delTTAinsCTG synonymous_variant 0.15
gyrA 8253 p.Ile318Leu missense_variant 0.15
gyrA 8264 c.963T>C synonymous_variant 0.15
gyrA 8270 c.969G>C synonymous_variant 0.14
gyrA 8366 c.1065G>C synonymous_variant 0.14
gyrA 8375 c.1074G>C synonymous_variant 0.14
gyrA 8462 c.1161A>G synonymous_variant 0.14
gyrA 8480 c.1179C>T synonymous_variant 0.12
fgd1 490955 p.Met58Arg missense_variant 0.98
rpoB 760925 c.1119T>C synonymous_variant 0.14
rpoB 760970 c.1164G>C synonymous_variant 0.15
rpoB 760982 c.1176G>C synonymous_variant 0.18
rpoB 760985 c.1179G>C synonymous_variant 0.18
rpoB 760991 c.1185G>C synonymous_variant 0.17
rpoB 761102 c.1296A>G synonymous_variant 0.14
rpoB 761150 c.1344A>C synonymous_variant 0.16
rpoB 761165 c.1359G>C synonymous_variant 0.16
rpoB 761168 c.1362C>G synonymous_variant 0.16
rpoB 761180 c.1374A>C synonymous_variant 0.16
rpoB 761222 c.1416G>C synonymous_variant 0.2
rpoB 761847 p.Cys681Ser missense_variant 0.13
rpoC 762989 c.-381G>C upstream_gene_variant 0.16
rpoC 762995 c.-375G>T upstream_gene_variant 0.15
rpoC 763028 c.-342T>C upstream_gene_variant 0.14
rpoC 763031 c.-339T>G upstream_gene_variant 0.14
rpoC 763034 c.-336C>G upstream_gene_variant 0.14
rpoC 763040 c.-330C>G upstream_gene_variant 0.14
rpoC 763070 c.-300T>C upstream_gene_variant 0.16
rpoC 763076 c.-294C>G upstream_gene_variant 0.16
rpoC 763528 c.159G>A synonymous_variant 0.12
rpoC 763658 c.289_291delCTTinsTTG synonymous_variant 0.13
rpoC 763675 c.306C>G synonymous_variant 0.14
rpoC 763732 c.363C>G synonymous_variant 0.13
rpoC 763780 c.411C>G synonymous_variant 0.12
rpoC 764405 c.1036A>C synonymous_variant 0.14
rpoC 764434 c.1065A>G synonymous_variant 0.16
rpoC 764446 c.1077T>C synonymous_variant 0.15
rpoC 764521 c.1152T>C synonymous_variant 0.16
rpoC 764830 c.1461C>G synonymous_variant 0.15
rpoC 764872 c.1503A>G synonymous_variant 0.16
rpoC 764893 c.1524T>C synonymous_variant 0.2
rpoC 764911 c.1542A>G synonymous_variant 0.18
rpoC 764923 c.1554A>G synonymous_variant 0.17
rpoC 764932 c.1563C>A synonymous_variant 0.16
rpoC 764968 c.1599T>C synonymous_variant 0.16
rpoC 764995 c.1626C>G synonymous_variant 0.15
rpoC 765007 c.1638T>G synonymous_variant 0.15
rpoC 765553 c.2184C>T synonymous_variant 0.12
rpoC 766657 c.3288A>G synonymous_variant 0.16
rpoC 766843 c.3474T>C synonymous_variant 0.16
rpoC 766861 c.3492G>C synonymous_variant 0.13
mmpS5 779639 c.-735dupG upstream_gene_variant 1.0
rplC 800612 c.-197A>G upstream_gene_variant 0.14
rplC 800618 c.-191T>C upstream_gene_variant 0.14
fbiC 1304529 c.1599T>C synonymous_variant 0.95
Rv1258c 1406845 p.Ala166Pro missense_variant 1.0
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.12
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.16
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.13
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.13
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.14
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.13
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.16
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.12
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.15
rrl 1473945 n.288T>C non_coding_transcript_exon_variant 0.15
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.15
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.14
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.13
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.33
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.45
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.45
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.44
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.44
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.51
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.51
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.51
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.51
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.51
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.51
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.51
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.53
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.51
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.54
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.52
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.51
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.51
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.46
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.43
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
inhA 1674607 p.Pro136Ser missense_variant 0.94
inhA 1674778 p.Pro193Ala missense_variant 0.97
rpsA 1833589 c.48A>T synonymous_variant 0.13
rpsA 1833619 c.78A>C synonymous_variant 0.19
rpsA 1833661 c.120A>G synonymous_variant 0.17
rpsA 1833667 c.126C>G synonymous_variant 0.18
rpsA 1833727 c.186G>C synonymous_variant 0.13
rpsA 1833787 c.246C>G synonymous_variant 0.14
rpsA 1833790 c.249T>A synonymous_variant 0.15
rpsA 1833799 c.258C>G synonymous_variant 0.15
rpsA 1833811 c.270G>C synonymous_variant 0.16
rpsA 1833862 c.321G>T synonymous_variant 0.13
rpsA 1833928 c.387G>C synonymous_variant 0.14
rpsA 1834474 c.933C>G synonymous_variant 0.13
rpsA 1834669 c.1128G>C synonymous_variant 0.13
rpsA 1834688 p.Ser383Cys missense_variant 0.13
PPE35 2169081 p.Leu511Ser missense_variant 1.0
PPE35 2169202 p.Ser471Pro missense_variant 1.0
Rv1979c 2222091 c.1074G>T synonymous_variant 1.0
Rv1979c 2223306 c.-142T>A upstream_gene_variant 1.0
pncA 2289228 p.Ile5Asn missense_variant 1.0
kasA 2518176 p.Ala21Gly missense_variant 1.0
kasA 2518642 c.528A>G synonymous_variant 0.14
kasA 2518663 c.549T>C synonymous_variant 0.13
kasA 2518687 c.573C>T synonymous_variant 0.13
kasA 2518741 c.627G>C synonymous_variant 0.16
kasA 2518747 c.633C>G synonymous_variant 0.18
eis 2714755 p.Pro193Gln missense_variant 1.0
ahpC 2726324 c.132A>G synonymous_variant 1.0
ahpC 2726362 p.Phe57Ser missense_variant 0.97
pepQ 2859580 p.Leu280Arg missense_variant 1.0
pepQ 2859999 c.420G>T synonymous_variant 1.0
thyX 3067940 c.6C>G synonymous_variant 1.0
thyA 3074620 c.-149C>A upstream_gene_variant 1.0
fprA 3473812 c.-195G>A upstream_gene_variant 0.13
fprA 3473861 c.-146T>G upstream_gene_variant 0.93
fprA 3474953 p.Gln316Arg missense_variant 1.0
rpoA 3878001 c.507A>G synonymous_variant 0.13
ddn 3986889 p.Phe16Val missense_variant 1.0
clpC1 4038444 p.Ala754Lys missense_variant 0.13
clpC1 4038446 c.2259T>C synonymous_variant 0.13
clpC1 4038452 c.2253G>C synonymous_variant 0.15
clpC1 4038461 p.Ala748Asp missense_variant 0.13
clpC1 4038596 c.2109A>G synonymous_variant 0.14
clpC1 4039694 c.1011G>C synonymous_variant 0.13
clpC1 4039724 c.981A>G synonymous_variant 0.18
clpC1 4040423 c.282A>G synonymous_variant 0.14
clpC1 4040426 c.279T>C synonymous_variant 0.14
embC 4242041 p.Met727Leu missense_variant 1.0
embA 4244723 p.Gln497His missense_variant 1.0
embA 4245083 c.1851A>C synonymous_variant 0.15
embA 4245137 c.1905T>C synonymous_variant 0.13
embB 4247491 c.978G>C synonymous_variant 0.14
embB 4247497 c.984T>C synonymous_variant 0.14
embB 4248118 c.1605T>C synonymous_variant 0.14
embB 4248127 c.1614G>C synonymous_variant 0.14
embB 4248133 c.1620C>G synonymous_variant 0.13
aftB 4267979 c.858G>C synonymous_variant 1.0