TB-Profiler result

Run: SRR13861163
Summary

Run ID: SRR13861163

Sample name:

Date: 03-04-2023 09:25:05

Number of reads: 795118

Percentage reads mapped: 26.53

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 0.99
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 5258 p.Lys7* stop_gained 1.0
gyrB 7122 c.1883_1884insA frameshift_variant 0.96
gyrA 9345 c.2044A>C synonymous_variant 0.15
gyrA 9374 c.2073G>C synonymous_variant 0.15
gyrA 9383 c.2082T>C synonymous_variant 0.17
gyrA 9386 c.2085T>C synonymous_variant 0.17
gyrA 9395 c.2094G>C synonymous_variant 0.18
gyrA 9413 c.2112G>C synonymous_variant 0.24
gyrA 9419 c.2118T>C synonymous_variant 0.15
gyrA 9420 p.Ile707Ala missense_variant 0.15
gyrA 9429 p.Arg710Tyr missense_variant 0.15
gyrA 9443 c.2142G>C synonymous_variant 0.17
gyrA 9449 c.2148C>G synonymous_variant 0.16
gyrA 9452 c.2151G>C synonymous_variant 0.15
gyrA 9455 c.2154T>C synonymous_variant 0.15
gyrA 9458 c.2157A>G synonymous_variant 0.14
gyrA 9467 c.2166T>C synonymous_variant 0.16
rpoB 761791 p.Arg662His missense_variant 0.12
rpoB 761864 c.2058G>C synonymous_variant 0.14
rpoB 761873 c.2067A>G synonymous_variant 0.16
rpoB 761885 c.2079T>C synonymous_variant 0.17
rpoB 761891 c.2085G>C synonymous_variant 0.16
rpoB 761906 c.2100C>G synonymous_variant 0.16
rpoB 761909 c.2103T>C synonymous_variant 0.15
rpoB 761912 c.2106T>C synonymous_variant 0.15
rpoB 761915 p.Asp703Glu missense_variant 0.15
rpoB 761916 p.Asp704Asn missense_variant 0.15
rpoC 762443 c.-927G>C upstream_gene_variant 0.12
rpoC 762995 c.-375G>T upstream_gene_variant 0.12
rpoC 763702 c.333C>G synonymous_variant 0.14
rpoC 763708 c.339G>A synonymous_variant 0.14
rpoC 763709 c.340C>T synonymous_variant 0.14
rpoC 763714 c.345G>C synonymous_variant 0.14
rpoC 763801 c.432C>G synonymous_variant 0.15
rpoC 763807 c.438T>C synonymous_variant 0.19
rpoC 763819 c.450G>C synonymous_variant 0.19
rpoC 763831 c.462A>G synonymous_variant 0.14
rpoC 763933 c.564C>T synonymous_variant 0.15
rpoC 763945 c.576T>C synonymous_variant 0.15
rpoC 763967 p.Gly200Ser missense_variant 0.15
rpoC 763978 c.609C>G synonymous_variant 0.16
rpoC 763996 c.627T>C synonymous_variant 0.16
rpoC 764011 c.642T>C synonymous_variant 0.14
rpoC 764024 c.655T>C synonymous_variant 0.14
rpoC 764040 p.Ser224Asn missense_variant 0.16
rpoC 764044 c.675T>C synonymous_variant 0.16
rpoC 764872 c.1503A>G synonymous_variant 0.14
rpoC 765349 c.1980T>C synonymous_variant 0.15
rpoC 765352 c.1983G>C synonymous_variant 0.14
rpoC 766381 c.3012C>T synonymous_variant 0.12
rpoC 766384 c.3015A>G synonymous_variant 0.12
rpoC 766390 c.3021C>T synonymous_variant 0.12
rpoC 766426 c.3057C>T synonymous_variant 0.13
rpoC 766447 c.3078T>C synonymous_variant 0.17
rpoC 766945 c.3576A>G synonymous_variant 0.12
rpoC 767035 c.3666G>T synonymous_variant 0.13
rpoC 767062 c.3693C>A synonymous_variant 0.12
rpoC 767119 c.3750A>G synonymous_variant 0.13
rpoC 767134 c.3765C>G synonymous_variant 0.13
rpoC 767167 c.3798C>G synonymous_variant 0.12
mmpL5 776374 p.Arg703Cys missense_variant 1.0
mmpR5 779126 p.Cys46Phe missense_variant 1.0
rpsL 781760 c.201T>C synonymous_variant 0.12
rplC 801447 p.Lys213Asn missense_variant 1.0
fbiC 1303004 p.Ala25Glu missense_variant 1.0
fbiC 1303171 p.Arg81Trp missense_variant 1.0
fbiC 1303517 p.Met196Thr missense_variant 0.96
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.12
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.26
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.29
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.29
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.29
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.29
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.29
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.29
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.31
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.3
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.3
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.29
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.29
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.29
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.28
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.29
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.29
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.26
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.14
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.15
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.14
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.14
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.13
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.18
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.17
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.14
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.17
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.18
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.14
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.14
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.17
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.16
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.17
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.16
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.14
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.15
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.16
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.22
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.56
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.64
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.64
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.66
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.67
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.71
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.7
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.7
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.68
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.69
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.72
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.71
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.73
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.73
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.71
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.7
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.64
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.64
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.64
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.62
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.28
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.15
inhA 1674507 c.306G>C synonymous_variant 0.15
inhA 1674537 c.336C>G synonymous_variant 0.19
inhA 1674542 p.Ala114Glu missense_variant 0.16
inhA 1674549 c.348G>C synonymous_variant 0.18
inhA 1674555 c.354G>A synonymous_variant 0.21
inhA 1674561 c.360C>T synonymous_variant 0.21
inhA 1674564 c.363C>T synonymous_variant 0.21
inhA 1674582 c.381T>C synonymous_variant 0.19
inhA 1674585 c.384T>C synonymous_variant 0.18
inhA 1674589 p.Met130Leu missense_variant 0.18
inhA 1674624 c.423A>C synonymous_variant 0.13
inhA 1674627 c.426T>G synonymous_variant 0.13
inhA 1674630 c.429C>G synonymous_variant 0.13
inhA 1674654 c.453G>C synonymous_variant 0.12
rpsA 1834366 c.825A>G synonymous_variant 0.15
rpsA 1834375 c.834G>A synonymous_variant 0.15
rpsA 1834465 c.924T>C synonymous_variant 0.14
rpsA 1834468 c.927A>G synonymous_variant 0.14
rpsA 1834489 c.948T>C synonymous_variant 0.17
rpsA 1834498 c.957C>T synonymous_variant 0.16
rpsA 1834528 c.987T>C synonymous_variant 0.15
rpsA 1834546 c.1005T>C synonymous_variant 0.14
rpsA 1834555 c.1014T>C synonymous_variant 0.15
rpsA 1834558 c.1017C>G synonymous_variant 0.14
rpsA 1834606 c.1065C>G synonymous_variant 0.17
rpsA 1834609 c.1068T>C synonymous_variant 0.17
rpsA 1834622 c.1081_1083delTCGinsAGC synonymous_variant 0.17
rpsA 1834633 c.1092A>G synonymous_variant 0.17
rpsA 1834639 c.1098T>C synonymous_variant 0.16
rpsA 1834640 p.Glu367* stop_gained 0.84
rpsA 1834688 c.1147_1148delAGinsTC synonymous_variant 0.13
rpsA 1834732 c.1191T>C synonymous_variant 0.16
rpsA 1834733 p.Ala398Pro missense_variant 0.16
ndh 2103004 c.39T>G synonymous_variant 1.0
katG 2155741 p.Gly124Asp missense_variant 0.12
PPE35 2170453 p.Gly54Ser missense_variant 1.0
Rv1979c 2223326 c.-162C>T upstream_gene_variant 1.0
pncA 2288748 p.Ala165Asp missense_variant 1.0
kasA 2517947 c.-168C>T upstream_gene_variant 0.18
kasA 2517974 c.-141T>C upstream_gene_variant 0.15
kasA 2517989 c.-126T>C upstream_gene_variant 0.13
kasA 2517992 c.-123C>G upstream_gene_variant 0.13
kasA 2517998 c.-117C>T upstream_gene_variant 0.16
kasA 2518474 p.Glu120Asp missense_variant 0.92
thyX 3067529 c.417C>G synonymous_variant 0.95
thyX 3067661 c.285C>G synonymous_variant 0.12
thyX 3067682 c.264G>C synonymous_variant 0.18
thyX 3067685 c.261A>G synonymous_variant 0.14
thyX 3067688 c.258G>C synonymous_variant 0.14
thyX 3067694 c.252G>C synonymous_variant 0.14
thyA 3073764 c.708T>C synonymous_variant 1.0
thyA 3073862 p.Gly204Ser missense_variant 1.0
thyA 3073963 p.Leu170Gln missense_variant 0.85
thyA 3073977 c.495A>G synonymous_variant 0.15
thyA 3073989 c.483T>C synonymous_variant 0.16
thyA 3074001 c.471C>G synonymous_variant 0.18
thyA 3074004 c.468T>C synonymous_variant 0.17
thyA 3074010 c.462C>G synonymous_variant 0.17
thyA 3074076 c.396C>G synonymous_variant 0.14
thyA 3074106 c.366T>C synonymous_variant 0.12
fbiD 3339357 c.240G>T synonymous_variant 1.0
Rv3083 3448352 c.-152G>C upstream_gene_variant 1.0
Rv3083 3449624 p.Lys374Met missense_variant 1.0
Rv3083 3449919 c.1416C>A synonymous_variant 0.95
fbiB 3642227 p.Gln231His missense_variant 1.0
fbiB 3642581 c.1047A>C synonymous_variant 1.0
rpoA 3877704 c.804G>T synonymous_variant 0.15
rpoA 3877743 c.765T>C synonymous_variant 0.15
rpoA 3878304 c.204G>C synonymous_variant 0.14
rpoA 3878313 c.195G>C synonymous_variant 0.14
rpoA 3878322 c.186A>G synonymous_variant 0.16
clpC1 4039831 c.874T>C synonymous_variant 0.14
clpC1 4039832 c.873C>G synonymous_variant 0.14
clpC1 4039850 c.855T>C synonymous_variant 0.14
clpC1 4039946 c.759A>T synonymous_variant 0.15
clpC1 4039952 c.753T>C synonymous_variant 0.13
clpC1 4039958 c.747G>C synonymous_variant 0.13
clpC1 4039996 p.Glu237Gln missense_variant 0.14
embA 4244641 p.Val470Gly missense_variant 1.0
embA 4245197 c.1965C>T synonymous_variant 0.96
embB 4246641 p.Ala43Glu missense_variant 1.0
embB 4247233 p.Asp240Glu missense_variant 1.0
ethA 4327035 p.Tyr147Asp missense_variant 1.0
ethR 4327923 p.Gln125His missense_variant 1.0