TB-Profiler result

Run: ERR2229354
Summary

Run ID: ERR2229354

Sample name:

Date: 31-03-2023 17:06:10

Number of reads: 1416522

Percentage reads mapped: 99.06

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575464 c.122_124dupCAG disruptive_inframe_insertion 0.12
mshA 576108 p.Ala254Gly missense_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775864 p.Ala873Ser missense_variant 0.2
mmpL5 775865 c.2616T>G synonymous_variant 0.13
mmpL5 775874 c.2607C>A synonymous_variant 0.13
mmpL5 775955 p.Ile842Val missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.13
mmpL5 777128 c.1353A>G synonymous_variant 0.13
mmpR5 779056 p.Met23Val missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304181 c.1251G>T synonymous_variant 0.13
Rv1258c 1406534 c.807C>A synonymous_variant 0.13
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.17
Rv1258c 1406946 p.Ala132Gly missense_variant 0.17
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.17
embR 1416805 c.543A>G synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
tlyA 1917809 c.-131G>T upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156007 p.Asn35Lys missense_variant 0.13
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2167965 p.Ala883Gly missense_variant 0.19
PPE35 2167967 c.2646A>C synonymous_variant 0.19
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.13
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169488 c.1125G>C synonymous_variant 0.14
PPE35 2169491 c.1122T>C synonymous_variant 0.14
PPE35 2169602 c.1011C>A synonymous_variant 0.15
PPE35 2169725 c.888T>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.52
PPE35 2170053 p.Thr187Ser missense_variant 0.51
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.13
kasA 2518879 c.765A>G synonymous_variant 0.24
kasA 2518882 c.768C>A synonymous_variant 0.24
eis 2715028 p.Ala102Val missense_variant 0.13
pepQ 2860552 c.-134C>A upstream_gene_variant 0.14
thyX 3067340 c.606G>A synonymous_variant 0.17
fbiD 3339744 c.627A>C synonymous_variant 0.2
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
alr 3841612 c.-193_-192insC upstream_gene_variant 0.15
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244184 p.Ser318Arg missense_variant 0.11
embA 4244854 p.Val541Gly missense_variant 0.18
embA 4245092 c.1860C>T synonymous_variant 0.14
embA 4245688 p.Val819Ala missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.39
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.36
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246563 p.Leu17Trp missense_variant 0.2
embB 4247470 c.957T>C synonymous_variant 0.13
embB 4248804 p.Met764Thr missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0