TB-Profiler result

Run: SRR13837615
Summary

Run ID: SRR13837615

Sample name:

Date: 03-04-2023 09:14:26

Number of reads: 297570

Percentage reads mapped: 97.22

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 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
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 760337 c.531C>G synonymous_variant 0.19
rpoB 760340 c.534G>C synonymous_variant 0.13
rpoB 760361 c.555T>C synonymous_variant 0.13
rpoB 760406 c.600G>C synonymous_variant 0.17
rpoB 760424 c.618C>G synonymous_variant 0.12
rpoB 760430 c.624T>C synonymous_variant 0.11
rpoB 760475 c.669A>G synonymous_variant 0.12
rpoB 760514 c.708C>T synonymous_variant 0.14
rpoB 760522 p.Ser239Asn missense_variant 0.13
rpoB 760728 p.Tyr308Asn missense_variant 1.0
rpoC 762827 c.-543G>C upstream_gene_variant 0.15
rpoC 763928 p.Glu187* stop_gained 1.0
rpoC 764923 c.1554A>G synonymous_variant 0.18
rpoC 764932 c.1563C>A synonymous_variant 0.22
rpoC 766155 p.Ala929Val missense_variant 1.0
mmpL5 777185 c.1296G>T synonymous_variant 1.0
rpsL 781793 c.234G>C synonymous_variant 0.2
rpsL 781929 p.Gly124Ser missense_variant 0.14
rplC 801174 c.366T>C synonymous_variant 0.17
fbiC 1302932 p.Val1Gly missense_variant 1.0
fbiC 1303151 p.Gly74Asp missense_variant 1.0
fbiC 1303995 c.1065C>T synonymous_variant 0.27
fbiC 1304001 c.1071C>G synonymous_variant 0.27
fbiC 1304008 c.1078T>C synonymous_variant 0.27
fbiC 1304034 c.1104A>G synonymous_variant 0.23
fbiC 1304040 c.1110C>G synonymous_variant 0.21
fbiC 1304046 c.1116C>G synonymous_variant 0.21
fbiC 1304049 c.1119T>G synonymous_variant 0.23
fbiC 1304058 c.1128G>A synonymous_variant 0.17
fbiC 1304059 c.1129C>T synonymous_variant 0.17
fbiC 1304064 c.1134G>C synonymous_variant 0.18
fbiC 1304073 c.1143C>T synonymous_variant 0.2
fbiC 1304080 p.Ala384Ser missense_variant 0.2
fbiC 1304091 p.Asp387Glu missense_variant 0.2
fbiC 1304092 p.Met388Leu missense_variant 0.17
fbiC 1304097 c.1167G>C synonymous_variant 0.18
fbiC 1304895 c.1965C>A synonymous_variant 1.0
fbiC 1305298 p.Lys790Gln missense_variant 0.93
Rv1258c 1406311 c.1030C>T synonymous_variant 1.0
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.22
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.22
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.22
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.12
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.15
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.18
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.18
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.2
inhA 1674379 c.178C>T synonymous_variant 0.17
inhA 1674382 p.Leu61Ile missense_variant 0.18
inhA 1674387 c.186A>G synonymous_variant 0.22
inhA 1674399 c.198A>G synonymous_variant 0.22
inhA 1674415 p.Ala72Asn missense_variant 0.2
inhA 1674419 p.Ser73Thr missense_variant 0.2
inhA 1674421 c.220T>C synonymous_variant 0.2
inhA 1674427 p.Gly76Gln missense_variant 0.2
inhA 1674440 p.Glu80Ala missense_variant 0.22
inhA 1674443 p.Ala81Glu missense_variant 0.22
inhA 1674450 c.249G>C synonymous_variant 0.25
inhA 1674452 p.Ala84Glu missense_variant 0.25
inhA 1674461 p.Lys87Arg missense_variant 0.22
inhA 1674480 c.279T>C synonymous_variant 0.2
inhA 1674507 c.306G>C synonymous_variant 0.22
inhA 1674542 p.Ala114Glu missense_variant 0.25
inhA 1674549 c.348G>C synonymous_variant 0.25
inhA 1674555 c.354G>A synonymous_variant 0.29
inhA 1674561 c.360C>T synonymous_variant 0.29
inhA 1674564 c.363C>T synonymous_variant 0.29
inhA 1674582 c.381T>C synonymous_variant 0.25
inhA 1674585 c.384T>C synonymous_variant 0.25
inhA 1674589 p.Met130Leu missense_variant 0.25
inhA 1674624 c.423A>C synonymous_variant 0.4
inhA 1674627 c.426T>G synonymous_variant 0.4
inhA 1674630 c.429C>G synonymous_variant 0.4
inhA 1674636 c.435C>G synonymous_variant 0.4
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 0.93