TB-Profiler result

Run: ERR2229689
Summary

Run ID: ERR2229689

Sample name:

Date: 31-03-2023 17:25:51

Number of reads: 894474

Percentage reads mapped: 99.19

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 6173 p.Glu312Lys missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7650 p.Gly117Ser missense_variant 0.12
mshA 575288 c.-60G>T upstream_gene_variant 0.12
mshA 576574 p.Cys409Trp missense_variant 0.12
rpoB 760736 c.930C>G synonymous_variant 0.1
rpoC 767274 p.Gly1302Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775834 p.Ala883Ser missense_variant 0.29
mmpL5 776931 p.Asp517Gly missense_variant 0.12
mmpL5 777101 c.1377_1379delGGC disruptive_inframe_deletion 0.18
mmpL5 777751 p.Arg244Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302767 c.-164G>C upstream_gene_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303786 c.859_860delAT frameshift_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476663 n.3006C>A non_coding_transcript_exon_variant 0.33
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
inhA 1674239 p.Ser13Ile missense_variant 0.15
rpsA 1833630 p.Ile30Asn missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917984 c.45C>A synonymous_variant 0.14
tlyA 1918131 c.192G>C synonymous_variant 0.12
katG 2153947 p.Gln722Arg missense_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.17
PPE35 2167967 c.2646A>C synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169287 c.1326T>C synonymous_variant 0.1
PPE35 2169308 c.1305C>T synonymous_variant 0.33
PPE35 2169322 c.1291T>C synonymous_variant 0.22
PPE35 2169323 c.1290C>G synonymous_variant 0.2
PPE35 2169326 c.1287C>T synonymous_variant 0.15
PPE35 2169570 p.Ser348Asn missense_variant 0.12
PPE35 2169578 c.1035T>C synonymous_variant 0.13
PPE35 2169605 p.Asn336Thr missense_variant 0.15
PPE35 2169624 p.Gly330Asp missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.79
PPE35 2170053 p.Thr187Ser missense_variant 0.79
PPE35 2170066 p.Ala183Thr missense_variant 0.27
PPE35 2170528 p.Ser29Ala missense_variant 0.12
PPE35 2170529 c.84G>C synonymous_variant 0.12
PPE35 2170535 c.78G>T synonymous_variant 0.14
PPE35 2170547 c.66A>G synonymous_variant 0.12
Rv1979c 2222758 p.Val136Ala missense_variant 0.12
Rv1979c 2222980 p.Ala62Glu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289877 c.-636C>G upstream_gene_variant 0.17
kasA 2518286 p.Val58Phe missense_variant 0.13
kasA 2518348 c.234A>T synonymous_variant 0.12
kasA 2519090 p.Ile326Phe missense_variant 0.29
eis 2714749 p.Val195Glu missense_variant 0.15
folC 2747273 p.Ser109* stop_gained 0.22
folC 2747507 p.Glu31Val missense_variant 0.15
Rv2752c 3064835 p.Ile453Phe missense_variant 0.14
thyX 3067351 p.Arg199Gly missense_variant 0.14
thyA 3074464 p.Pro3Leu missense_variant 0.2
fprA 3474248 p.Asn81Ser missense_variant 0.22
Rv3236c 3612677 p.Glu147Gly missense_variant 0.12
Rv3236c 3613052 p.Gly22Asp missense_variant 0.12
fbiB 3642519 p.Asp329Asn missense_variant 0.14
alr 3840992 c.429C>T synonymous_variant 0.12
rpoA 3877741 p.Leu256Pro missense_variant 0.1
clpC1 4038919 p.Gly596Ser missense_variant 0.11
embC 4241061 p.Pro400Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245074 c.1842G>C synonymous_variant 0.11
embA 4246081 p.Pro950His missense_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.45
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.45
embB 4246563 p.Leu17Trp missense_variant 0.44
embB 4246567 c.54G>T synonymous_variant 0.57
embB 4247475 p.Arg321Leu missense_variant 0.12
embB 4247571 p.Pro353Gln missense_variant 0.18
embB 4247576 c.1063_1064insA frameshift_variant 0.18
aftB 4267963 c.873delT frameshift_variant 0.17
ethA 4326380 p.Thr365Lys missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0