TB-Profiler result

Run: SRR13861686
Summary

Run ID: SRR13861686

Sample name:

Date: 03-04-2023 09:38:05

Number of reads: 258886

Percentage reads mapped: 25.91

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 761131 p.Gly442Glu missense_variant 0.18 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 6209 c.970C>T synonymous_variant 0.22
gyrB 6214 c.975G>C synonymous_variant 0.2
gyrB 6217 c.978G>C synonymous_variant 0.2
gyrB 6223 c.984G>C synonymous_variant 0.22
gyrB 6242 p.Arg335Lys missense_variant 0.18
gyrB 6250 c.1011A>G synonymous_variant 0.18
gyrB 6253 c.1014G>C synonymous_variant 0.17
gyrB 6280 c.1041T>C synonymous_variant 0.18
gyrB 6286 c.1047T>C synonymous_variant 0.18
gyrB 6292 c.1053G>C synonymous_variant 0.18
gyrB 6295 c.1056A>G synonymous_variant 0.18
gyrB 6298 c.1059C>T synonymous_variant 0.18
gyrB 6299 c.1060C>T synonymous_variant 0.18
gyrA 6307 c.-995T>G upstream_gene_variant 0.18
gyrA 6319 c.-983G>C upstream_gene_variant 0.17
gyrA 6325 c.-977C>G upstream_gene_variant 0.17
gyrA 7799 c.498A>G synonymous_variant 0.18
gyrA 8020 p.Thr240Ile missense_variant 0.18
gyrA 8024 c.723T>C synonymous_variant 0.18
gyrA 8027 c.726T>C synonymous_variant 0.2
gyrA 8036 c.735A>G synonymous_variant 0.22
gyrA 8039 c.738T>C synonymous_variant 0.22
gyrA 8048 c.747C>T synonymous_variant 0.2
gyrA 8054 c.753T>C synonymous_variant 0.2
gyrA 8057 c.756A>G synonymous_variant 0.2
gyrA 8069 c.768T>C synonymous_variant 0.18
gyrA 8078 c.777A>G synonymous_variant 0.18
gyrA 8090 c.789C>G synonymous_variant 0.2
gyrA 8096 c.795T>C synonymous_variant 0.2
gyrA 8099 c.798T>C synonymous_variant 0.2
gyrA 8111 c.810G>C synonymous_variant 0.2
gyrA 8156 c.855T>C synonymous_variant 0.22
gyrA 8168 c.867A>G synonymous_variant 0.25
gyrA 8174 c.873C>G synonymous_variant 0.25
gyrA 8177 c.876A>C synonymous_variant 0.25
gyrA 8198 c.897T>C synonymous_variant 0.33
gyrA 8204 c.903C>T synonymous_variant 0.33
gyrA 8207 c.906T>C synonymous_variant 0.33
gyrA 8216 c.915G>A synonymous_variant 0.33
gyrA 8219 c.918T>C synonymous_variant 0.33
gyrA 8225 c.924T>C synonymous_variant 0.33
gyrA 8234 c.933T>G synonymous_variant 0.29
gyrA 8235 c.934_936delTTAinsCTG synonymous_variant 0.29
gyrA 8253 p.Ile318Leu missense_variant 0.25
gyrA 8264 c.963T>C synonymous_variant 0.25
gyrA 8267 c.966G>C synonymous_variant 0.25
gyrA 8270 c.969G>C synonymous_variant 0.25
gyrA 9023 c.1722A>C synonymous_variant 0.22
ccsA 620331 c.441C>T synonymous_variant 0.15
ccsA 620340 c.450C>G synonymous_variant 0.17
ccsA 620373 c.483C>G synonymous_variant 0.15
rpoB 760328 c.522G>C synonymous_variant 0.14
rpoB 760331 c.525G>C synonymous_variant 0.14
rpoB 760337 c.531C>G synonymous_variant 0.14
rpoB 760340 c.534G>C synonymous_variant 0.14
rpoB 760361 c.555T>C synonymous_variant 0.14
rpoB 760376 p.Asp190Glu missense_variant 0.14
rpoB 760406 c.600G>C synonymous_variant 0.18
rpoB 760418 c.612G>C synonymous_variant 0.2
rpoB 760424 c.618C>G synonymous_variant 0.17
rpoB 760430 c.624T>C synonymous_variant 0.17
rpoB 760547 c.741G>C synonymous_variant 0.22
rpoB 760563 p.Arg253Met missense_variant 0.33
rpoB 760591 p.Val262Ala missense_variant 0.43
rpoB 760611 c.805T>C synonymous_variant 0.5
rpoB 760634 c.828T>C synonymous_variant 0.43
rpoB 760646 c.840C>G synonymous_variant 0.33
rpoB 760655 c.849A>G synonymous_variant 0.33
rpoB 760661 c.855A>C synonymous_variant 0.33
rpoB 760670 c.864G>C synonymous_variant 0.33
rpoB 760674 c.868T>C synonymous_variant 0.33
rpoB 760679 c.873A>G synonymous_variant 0.5
rpoB 760683 c.877T>C synonymous_variant 0.4
rpoB 760718 c.912C>G synonymous_variant 0.33
rpoB 760721 c.915C>G synonymous_variant 0.33
rpoB 760724 c.918T>C synonymous_variant 0.33
rpoB 760730 c.924T>C synonymous_variant 0.33
rpoB 760751 c.945G>C synonymous_variant 0.29
rpoB 760757 c.951T>C synonymous_variant 0.25
rpoB 760759 p.Val318Ala missense_variant 0.25
rpoB 760763 c.957C>T synonymous_variant 0.25
rpoB 760769 c.963C>G synonymous_variant 0.25
rpoB 760775 c.969G>C synonymous_variant 0.29
rpoB 760776 c.970_972delTCGinsAGC synonymous_variant 0.25
rpoB 760793 c.987A>G synonymous_variant 0.25
rpoB 760805 c.999G>C synonymous_variant 0.25
rpoB 760817 c.1011A>G synonymous_variant 0.25
rpoB 760820 c.1014T>C synonymous_variant 0.25
rpoB 761126 c.1320G>T synonymous_variant 0.18
rpoB 761129 c.1323G>C synonymous_variant 0.18
rpoB 761133 p.Leu443Ile missense_variant 0.18
rpoB 761150 c.1344A>C synonymous_variant 0.2
rpoB 761151 p.Leu449Val missense_variant 0.2
rpoB 761156 c.1350G>C synonymous_variant 0.2
rpoB 761162 c.1356G>C synonymous_variant 0.2
rpoB 761165 c.1359G>C synonymous_variant 0.2
rpoB 761168 c.1362C>G synonymous_variant 0.18
rpoB 761178 p.Ser458Thr missense_variant 0.18
rpoB 761192 c.1386C>G synonymous_variant 0.18
rpoB 761195 c.1389G>C synonymous_variant 0.18
rpoB 761196 p.Leu464Phe missense_variant 0.18
rpoB 761204 c.1398C>T synonymous_variant 0.18
rpoB 761207 c.1401C>T synonymous_variant 0.18
rpoB 761213 c.1407G>A synonymous_variant 0.18
rpoB 761220 p.Ser472Thr missense_variant 0.18
rpoB 761234 c.1428G>C synonymous_variant 0.18
rpoB 761235 p.Met477Val missense_variant 0.18
rpoC 764387 c.1018T>C synonymous_variant 0.18
rpoC 764401 c.1032C>T synonymous_variant 0.18
rpoC 764404 c.1035C>T synonymous_variant 0.18
rpoC 764405 c.1036A>C synonymous_variant 0.27
rpoC 764419 c.1050C>T synonymous_variant 0.22
rpoC 764428 c.1059G>T synonymous_variant 0.2
rpoC 764434 c.1065A>G synonymous_variant 0.3
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.3
rpoC 764441 p.Ile358Leu missense_variant 0.2
rpoC 764446 c.1077T>C synonymous_variant 0.33
rpoC 764451 p.Gly361Ala missense_variant 0.22
rpoC 764455 c.1086G>T synonymous_variant 0.29
rpoC 764461 p.Glu364Asp missense_variant 0.29
rpoC 764470 c.1101C>G synonymous_variant 0.25
rpoC 764471 p.Asn368Arg missense_variant 0.25
rpoC 764479 c.1110G>A synonymous_variant 0.22
rpoC 764485 c.1116G>C synonymous_variant 0.25
rpoC 764498 p.Ser377Ala missense_variant 0.25
rpoC 764503 c.1134G>C synonymous_variant 0.22
rpoC 764509 c.1140G>C synonymous_variant 0.2
rpoC 764513 p.Phe382Leu missense_variant 0.2
rpoC 764521 c.1152T>C synonymous_variant 0.3
rpoC 766843 c.3474T>C synonymous_variant 0.15
rpoC 766861 c.3492G>C synonymous_variant 0.17
rpoC 766864 c.3495G>C synonymous_variant 0.17
rpoC 767098 c.3729T>C synonymous_variant 0.14
rpoC 767119 c.3750A>G synonymous_variant 0.12
rpsL 781736 c.177T>C synonymous_variant 0.3
rpsL 781751 c.192G>C synonymous_variant 0.25
rpsL 781754 c.195G>C synonymous_variant 0.25
rpsL 781760 c.201T>C synonymous_variant 0.25
rpsL 781793 c.234G>C synonymous_variant 0.25
rpsL 781832 c.273T>C synonymous_variant 0.22
rpsL 781841 c.282C>G synonymous_variant 0.22
rpsL 781859 c.300T>C synonymous_variant 0.22
rpsL 781868 c.309T>C synonymous_variant 0.2
rpsL 781871 c.312G>C synonymous_variant 0.2
rpsL 781929 p.Gly124Ser missense_variant 0.25
rplC 800612 c.-197A>G upstream_gene_variant 0.25
rplC 800618 c.-191T>C upstream_gene_variant 0.2
rplC 800648 c.-161A>C upstream_gene_variant 0.2
rplC 800654 c.-155T>C upstream_gene_variant 0.2
rplC 800693 c.-116A>G upstream_gene_variant 0.25
rplC 800703 c.-106T>C upstream_gene_variant 0.22
rplC 800715 c.-94A>C upstream_gene_variant 0.22
rplC 800720 c.-89T>C upstream_gene_variant 0.29
rplC 800723 c.-86C>G upstream_gene_variant 0.25
rplC 800738 c.-71T>C upstream_gene_variant 0.2
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.5
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.5
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.5
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.5
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.43
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.43
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.43
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.43
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.33
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.33
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.33
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.33
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.38
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.38
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.33
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.22
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.33
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.33
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.33
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.13
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.13
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.14
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.17
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.17
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.17
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.31
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.25
rrl 1473945 n.288T>C non_coding_transcript_exon_variant 0.25
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.27
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.27
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.27
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.25
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.57
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.6
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.6
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.64
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.62
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.67
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.7
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.65
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.7
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.7
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.7
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.67
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.67
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.7
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.7
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.78
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.78
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.78
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.82
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.45
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.3
inhA 1674216 c.15G>C synonymous_variant 0.29
inhA 1674231 c.30T>C synonymous_variant 0.29
inhA 1674237 c.36T>C synonymous_variant 0.29
inhA 1674239 p.Ser13Thr missense_variant 0.29
inhA 1674243 c.42A>G synonymous_variant 0.29
inhA 1674279 c.78A>C synonymous_variant 0.33
inhA 1674280 p.Arg27Lys missense_variant 0.33
inhA 1674285 c.84A>G synonymous_variant 0.33
inhA 1674301 c.102_103delCC frameshift_variant 0.33
inhA 1674307 c.106C>T synonymous_variant 0.33
inhA 1674315 c.114C>G synonymous_variant 0.29
inhA 1674321 c.120G>C synonymous_variant 0.29
rpsA 1833851 p.Lys104Gln missense_variant 1.0
Rv1979c 2223241 c.-77C>G upstream_gene_variant 1.0
pncA 2289811 c.-570C>T upstream_gene_variant 1.0
pncA 2289994 c.-753A>C upstream_gene_variant 1.0
kasA 2518301 p.His63Asp missense_variant 1.0
pepQ 2859859 p.Ala187Glu missense_variant 1.0
Rv2752c 3064886 p.Ala436Pro missense_variant 1.0
Rv2752c 3065258 p.Met312Val missense_variant 1.0
Rv3083 3449104 p.Pro201Ala missense_variant 1.0
Rv3236c 3612337 c.779delG frameshift_variant 1.0
fbiB 3641723 c.189T>C synonymous_variant 1.0
rpoA 3877740 c.768G>T synonymous_variant 1.0
embC 4241005 c.1143G>T synonymous_variant 1.0
embC 4241081 c.1220delT frameshift_variant 1.0
embC 4242746 p.Pro962Ser missense_variant 1.0
embA 4243969 p.Val246Ala missense_variant 1.0
embB 4248206 p.Ser565Gly missense_variant 0.22
embB 4248220 c.1707A>G synonymous_variant 0.22
embB 4248343 c.1830G>C synonymous_variant 0.22