TB-Profiler result

Run: ERR2229688
Summary

Run ID: ERR2229688

Sample name:

Date: 31-03-2023 17:26:11

Number of reads: 997631

Percentage reads mapped: 99.1

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 6557 p.Gly440Ser missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7836 p.Gly179Ser missense_variant 0.12
fgd1 491238 c.456C>T synonymous_variant 0.29
fgd1 491313 c.531C>T synonymous_variant 0.17
mshA 575648 p.Val101Met missense_variant 0.11
mshA 576680 p.Ile445Leu missense_variant 0.17
mshA 576693 p.Asn449Ile missense_variant 0.14
mshA 576700 p.Glu451Asp missense_variant 0.2
ccsA 619755 c.-136T>A upstream_gene_variant 0.17
rpoB 759850 p.Pro15Leu missense_variant 0.13
rpoB 761152 p.Leu449Gln missense_variant 0.22
rpoC 764532 p.Gly388Ala missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777124 p.Asp453Asn missense_variant 0.14
mmpL5 777151 p.Asn444Tyr missense_variant 0.17
mmpR5 779106 p.Leu39Phe missense_variant 0.15
mmpR5 779308 p.Arg107Gly missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303088 p.Asp53Gly missense_variant 0.12
fbiC 1303466 p.Ile179Asn missense_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304332 p.Ser468Gly missense_variant 0.12
fbiC 1304976 p.Lys682Asn missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475220 n.1563G>T non_coding_transcript_exon_variant 0.33
rrl 1475276 n.1623delG non_coding_transcript_exon_variant 0.4
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.1
fabG1 1673361 c.-79C>G upstream_gene_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3
fabG1 1673641 p.Val68Phe missense_variant 0.12
inhA 1674571 p.Ala124Thr missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.16
katG 2154735 c.1377G>A synonymous_variant 0.15
katG 2155282 p.Gly277Val missense_variant 0.12
PPE35 2168394 p.Ser740Ile missense_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168901 p.Pro571Leu missense_variant 0.12
PPE35 2169029 p.Asp528Glu missense_variant 0.2
PPE35 2169445 p.Gly390Cys missense_variant 0.2
PPE35 2169457 p.His386Asn missense_variant 0.14
PPE35 2169578 c.1035T>C synonymous_variant 0.13
PPE35 2169628 p.Ile329Val missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.6
PPE35 2170415 c.198A>G synonymous_variant 0.13
Rv1979c 2222317 p.Ala283Asp missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289676 c.-435T>C upstream_gene_variant 0.11
folC 2746667 p.Ala311Asp missense_variant 0.2
folC 2746959 p.Gly214Trp missense_variant 0.2
pepQ 2859428 p.Pro331Thr missense_variant 0.15
pepQ 2860480 c.-62G>A upstream_gene_variant 0.17
Rv2752c 3064907 p.Val429Ile missense_variant 0.13
thyX 3067340 c.606G>A synonymous_variant 0.16
whiB7 3568422 c.258G>T synonymous_variant 0.13
Rv3236c 3612499 c.618C>T synonymous_variant 0.33
fbiA 3641453 p.Arg304Gln missense_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3877764 c.744C>T synonymous_variant 0.12
clpC1 4039036 p.Val557Phe missense_variant 0.13
clpC1 4039594 p.Arg371Gly missense_variant 0.18
clpC1 4039602 p.Ala368Val missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.46
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4246563 p.Leu17Trp missense_variant 0.56
embB 4246567 c.54G>T synonymous_variant 0.56
embB 4246760 p.Val83Met missense_variant 0.12
embB 4247105 p.Pro198Ala missense_variant 0.18
embB 4247574 p.Asp354Val missense_variant 0.14
embB 4249688 c.3176delG frameshift_variant 0.29
aftB 4268470 p.Leu123Met missense_variant 0.11
aftB 4269327 c.-491A>G upstream_gene_variant 0.12
whiB6 4338224 p.Glu100Lys missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407654 c.549G>T synonymous_variant 0.12
gid 4407768 c.435G>A synonymous_variant 0.17
gid 4407816 c.387C>A synonymous_variant 0.14
gid 4407884 p.Asp107Asn missense_variant 0.14
gid 4407911 p.Thr98Ser missense_variant 0.14
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0