TB-Profiler result

Run: SRR13861196
Summary

Run ID: SRR13861196

Sample name:

Date: 03-04-2023 09:25:54

Number of reads: 824597

Percentage reads mapped: 20.64

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 0.14 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
rpoB 760728 p.Tyr308Asn missense_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.15
rpoB 761129 c.1323G>C synonymous_variant 0.15
rpoB 761133 p.Leu443Ile missense_variant 0.14
rpoB 761150 c.1344A>C synonymous_variant 0.15
rpoB 761151 p.Leu449Val missense_variant 0.15
rpoB 761156 c.1350G>C synonymous_variant 0.15
rpoB 761162 c.1356G>C synonymous_variant 0.16
rpoB 761165 c.1359G>C synonymous_variant 0.16
rpoB 761168 c.1362C>G synonymous_variant 0.2
rpoB 761178 p.Ser458Thr missense_variant 0.17
rpoB 761192 c.1386C>G synonymous_variant 0.17
rpoB 761195 c.1389G>C synonymous_variant 0.17
rpoB 761196 p.Leu464Phe missense_variant 0.17
rpoB 761204 c.1398C>T synonymous_variant 0.17
rpoB 761207 c.1401C>T synonymous_variant 0.17
rpoB 761213 c.1407G>A synonymous_variant 0.17
rpoB 761220 p.Ser472Thr missense_variant 0.17
rpoB 761234 c.1428G>C synonymous_variant 0.18
rpoB 761235 p.Met477Val missense_variant 0.2
rpoC 763928 p.Glu187* stop_gained 1.0
rpoC 766155 p.Ala929Val missense_variant 1.0
mmpL5 777185 c.1296G>T synonymous_variant 1.0
fbiC 1302932 p.Val1Gly missense_variant 1.0
fbiC 1303151 p.Gly74Asp missense_variant 1.0
fbiC 1304895 c.1965C>A synonymous_variant 1.0
fbiC 1305298 p.Lys790Gln missense_variant 1.0
Rv1258c 1406311 c.1030C>T synonymous_variant 0.96
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.21
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.25
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.25
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.25
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.24
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.24
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.23
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.24
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.23
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.24
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.24
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.24
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.24
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.25
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.23
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.24
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.2
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.52
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.61
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.61
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.61
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.61
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.66
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.66
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.65
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.65
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.65
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.66
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.65
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.66
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.68
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.67
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.68
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 0.64
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
rpsA 1834275 p.Ile245Thr missense_variant 1.0
tlyA 1917936 c.-4C>A upstream_gene_variant 1.0
ndh 2101676 p.Ala456Val missense_variant 1.0
pncA 2289356 c.-115G>T upstream_gene_variant 1.0
kasA 2518234 p.Glu40Asp missense_variant 1.0
Rv2752c 3064837 p.Leu452Trp missense_variant 1.0
Rv3083 3449643 p.Asn380Lys missense_variant 1.0
fprA 3474752 p.Ile249Ser missense_variant 1.0
fprA 3475315 p.His437Asn missense_variant 1.0
Rv3236c 3611967 p.Ser384Pro missense_variant 1.0
rpoA 3877756 p.Ile251Thr missense_variant 1.0
rpoA 3878065 p.Pro148Arg missense_variant 1.0
ddn 3986977 p.Pro45Arg missense_variant 1.0
clpC1 4040538 p.Leu56Arg missense_variant 1.0
embA 4245342 p.Ser704Pro missense_variant 1.0
embB 4248711 c.2198_2199insT frameshift_variant 1.0
aftB 4267498 p.Glu447Lys missense_variant 1.0
aftB 4268559 p.Leu93Gln missense_variant 1.0