TB-Profiler result

Run: SRR6045860
Summary

Run ID: SRR6045860

Sample name:

Date: 04-04-2023 12:06:39

Number of reads: 269951

Percentage reads mapped: 93.86

Strain: lineage4.1.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1.2 Euro-American (X-type) X1 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
gyrB 5205 c.-35G>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491014 p.Thr78Pro missense_variant 0.5
fgd1 491027 p.Asn82Thr missense_variant 0.5
rpoB 760197 p.Ala131Ser missense_variant 0.2
rpoB 761411 c.1605G>A synonymous_variant 0.4
rpoB 763042 p.Leu1079Pro missense_variant 0.22
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776152 p.Met777Val missense_variant 0.14
mmpS5 778616 c.252_289delAGCCCTGCCGTGGTCGCTCACCTTGAAGACCACGGCGC frameshift_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302814 c.-117C>T upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.4
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.4
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.4
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.4
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.4
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.25
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.38
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.38
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.29
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.33
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.33
rrl 1476706 n.3049C>T non_coding_transcript_exon_variant 0.29
fabG1 1673560 p.Lys41Leu missense_variant 0.29
tlyA 1918144 p.Lys69Arg missense_variant 0.2
tlyA 1918152 c.213C>T synonymous_variant 0.2
tlyA 1918153 p.Gly72Cys missense_variant 0.2
PPE35 2167745 p.Thr956Arg missense_variant 0.4
PPE35 2169902 p.Leu237Phe missense_variant 0.25
PPE35 2169910 p.Asn235Tyr missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518392 p.Gln93Leu missense_variant 0.14
kasA 2518395 p.Leu94Pro missense_variant 0.13
kasA 2518398 p.Trp95* stop_gained 0.13
kasA 2518400 p.Glu96Leu missense_variant 0.13
kasA 2518820 p.Gly236Ser missense_variant 0.25
eis 2714846 p.Val163Ile missense_variant 0.25
ahpC 2726338 p.Val49Gly missense_variant 0.33
ribD 2987189 c.351G>A synonymous_variant 0.33
ribD 2987451 c.614_616delGTG disruptive_inframe_deletion 0.29
ribD 2987458 c.620_621insCAC disruptive_inframe_insertion 0.25
Rv2752c 3064611 p.Ile527Asp missense_variant 0.25
thyA 3074645 c.-174T>G upstream_gene_variant 0.25
thyA 3074648 c.-177T>G upstream_gene_variant 0.43
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338922 c.-196G>T upstream_gene_variant 0.17
fbiD 3339273 c.156T>G synonymous_variant 0.29
Rv3083 3449787 c.1284C>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642047 c.513G>C synonymous_variant 0.4
clpC1 4038241 p.Gly822Ser missense_variant 0.14
clpC1 4039484 c.1221T>G synonymous_variant 0.33
embC 4241572 c.1710C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242872 p.Asp1004Asn missense_variant 0.33
embA 4243833 p.Ala201Thr missense_variant 1.0
embA 4244954 c.1722C>T synonymous_variant 0.29
embA 4246012 p.Phe927Ser missense_variant 0.33
embB 4246930 p.Gln139His missense_variant 1.0
embB 4247106 p.Pro198Arg missense_variant 0.18
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269748 p.Asn29Thr missense_variant 0.25
ethR 4327240 c.-309G>A upstream_gene_variant 0.2
ethA 4327359 p.Glu39Gln missense_variant 0.18
ethA 4328400 c.-927C>T upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407724 p.Leu160Pro missense_variant 0.33
gid 4408012 p.Arg64Gln missense_variant 0.11