TB-Profiler result

Run: ERR2229444
Summary

Run ID: ERR2229444

Sample name:

Date: 31-03-2023 17:11:52

Number of reads: 730129

Percentage reads mapped: 98.85

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 6747 p.Gln503Arg missense_variant 0.17
gyrB 6771 p.Thr511Ile missense_variant 0.17
gyrB 7120 c.1884delC frameshift_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8626 p.Arg442His missense_variant 0.14
gyrA 8822 p.Asp507Glu missense_variant 0.18
mshA 575265 c.-83C>A upstream_gene_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.29
mshA 576547 p.Asp400Glu missense_variant 0.17
mshA 576616 c.1269G>A synonymous_variant 0.11
rpoC 766798 c.3429C>A synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775822 p.Val887Leu missense_variant 0.13
mmpL5 776196 p.Ala762Glu missense_variant 0.12
mmpL5 776221 p.Ser754Pro missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800779 c.-30T>C upstream_gene_variant 0.15
rplC 800983 p.Pro59Gln missense_variant 0.14
fbiC 1303444 c.516dupC frameshift_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406429 c.912C>G synonymous_variant 0.11
atpE 1461043 c.-2A>G upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473043 n.1202dupC non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474740 n.1083G>T non_coding_transcript_exon_variant 0.29
rrl 1474940 n.1283C>T non_coding_transcript_exon_variant 0.15
rrl 1475573 n.1921delC non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.43
rpsA 1834218 p.Val226Ala missense_variant 0.12
tlyA 1917876 c.-64C>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101708 c.1335G>T synonymous_variant 0.15
ndh 2103001 c.42G>A synonymous_variant 0.14
katG 2155810 p.Leu101Gln missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168809 p.Val602Ile missense_variant 0.12
PPE35 2169215 p.Glu466Asp missense_variant 0.12
PPE35 2169902 c.711G>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2222797 p.Pro123Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518230 p.Gly39Val missense_variant 0.12
kasA 2518809 p.Lys232Arg missense_variant 0.25
eis 2714771 p.Gly188Cys missense_variant 0.14
ahpC 2726470 c.281delT frameshift_variant 0.15
pepQ 2860373 p.Ala16Thr missense_variant 0.15
thyA 3074272 p.Ser67Tyr missense_variant 0.12
ald 3086852 p.Asn11Lys missense_variant 0.15
Rv3083 3448481 c.-23G>T upstream_gene_variant 0.33
fprA 3474038 p.Ser11Tyr missense_variant 0.12
whiB7 3568626 c.53delT frameshift_variant 0.12
Rv3236c 3612618 p.Pro167Ser missense_variant 0.18
Rv3236c 3612881 p.Ala79Val missense_variant 0.18
Rv3236c 3613183 c.-67C>A upstream_gene_variant 0.22
fbiB 3641190 c.-345G>C upstream_gene_variant 0.12
fbiB 3642639 p.Glu369* stop_gained 0.18
fbiB 3642695 c.1161G>A synonymous_variant 0.29
rpoA 3878166 c.342C>G synonymous_variant 0.18
ddn 3986693 c.-150delG upstream_gene_variant 0.15
ddn 3986711 c.-133C>T upstream_gene_variant 0.15
clpC1 4039730 c.975C>G synonymous_variant 0.16
clpC1 4040144 c.561G>C synonymous_variant 0.22
clpC1 4040359 c.344_345delAG frameshift_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246154 c.-360G>A upstream_gene_variant 0.4
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.47
embB 4246555 c.42G>C synonymous_variant 0.54
embB 4246556 p.Ala15Pro missense_variant 0.54
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.29
embB 4246747 p.Asp78Glu missense_variant 0.18
embB 4247153 p.Pro214Ser missense_variant 0.2
embB 4247176 c.663G>C synonymous_variant 0.15
embB 4249378 c.2865G>T synonymous_variant 0.12
embB 4249682 c.3172delG frameshift_variant 0.25
aftB 4268529 p.Gly103Asp missense_variant 0.15
ubiA 4268974 p.Leu287Gln missense_variant 0.15
ethA 4327281 p.Arg65* stop_gained 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0