TB-Profiler result

Run: SRR21677874
Summary

Run ID: SRR21677874

Sample name:

Date: 04-04-2023 02:49:12

Number of reads: 167884

Percentage reads mapped: 98.52

Strain:

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
lineage4.1.1.2 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 5191 c.-49G>T upstream_gene_variant 0.33
gyrA 6520 c.-782G>A upstream_gene_variant 1.0
gyrB 6845 p.Asp536Tyr missense_variant 0.33
gyrA 7024 c.-278G>A upstream_gene_variant 0.4
gyrB 7044 p.Asn602Ser missense_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8857 p.Thr519Ile missense_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9416 c.2115C>T synonymous_variant 0.22
fgd1 491177 p.Leu132Pro missense_variant 0.33
fgd1 491777 p.Leu332Trp missense_variant 0.33
mshA 575280 c.-68G>T upstream_gene_variant 0.4
ccsA 619704 c.-187G>A upstream_gene_variant 1.0
ccsA 620296 p.Pro136Ser missense_variant 0.25
ccsA 620340 c.450C>T synonymous_variant 0.2
rpoB 761184 p.Glu460Lys missense_variant 0.29
rpoC 763810 p.Glu147Asp missense_variant 0.33
rpoC 764822 p.Asp485His missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765271 p.Lys634Asn missense_variant 0.4
rpoC 765827 p.Met820Val missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776147 c.2334C>T synonymous_variant 0.67
mmpL5 776273 c.2208C>G synonymous_variant 0.5
mmpL5 777128 c.1353A>G synonymous_variant 0.22
mmpL5 778927 c.-447C>A upstream_gene_variant 0.33
mmpR5 779040 p.Met17Ile missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302814 c.-117C>T upstream_gene_variant 1.0
fbiC 1304537 p.Arg536Leu missense_variant 0.33
Rv1258c 1406111 p.Asp410Glu missense_variant 0.14
embR 1416484 c.864G>A synonymous_variant 0.14
embR 1416734 c.613delG frameshift_variant 0.29
embR 1416850 c.498G>A synonymous_variant 0.12
embR 1416874 p.Phe158Leu missense_variant 0.12
embR 1417247 p.Lys34Arg missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472520 n.675T>C non_coding_transcript_exon_variant 0.15
rrl 1474287 n.630T>C non_coding_transcript_exon_variant 0.29
fabG1 1673503 p.Gly22* stop_gained 0.5
inhA 1673640 c.-562C>T upstream_gene_variant 0.2
fabG1 1673735 p.Arg99Leu missense_variant 0.4
rpsA 1833802 p.Glu87Asp missense_variant 0.5
rpsA 1834700 c.1160delA frameshift_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102275 c.768C>A synonymous_variant 0.33
katG 2154515 p.Pro533Thr missense_variant 0.33
katG 2156084 p.Glu10Lys missense_variant 0.11
katG 2156113 c.-2C>T upstream_gene_variant 0.12
katG 2156245 c.-134G>A upstream_gene_variant 0.14
PPE35 2168575 p.Ala680Ser missense_variant 0.33
Rv1979c 2222496 c.669G>T synonymous_variant 0.18
Rv1979c 2222740 p.Leu142Pro missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289273 c.-32C>A upstream_gene_variant 0.12
pncA 2289897 c.-656G>T upstream_gene_variant 1.0
kasA 2518215 p.Lys34Arg missense_variant 0.18
kasA 2518250 p.Leu46Ile missense_variant 0.29
kasA 2518373 p.Gly87Arg missense_variant 0.29
eis 2714195 p.Ser380Pro missense_variant 0.25
eis 2714222 p.Ala371Ser missense_variant 0.5
ahpC 2726202 p.Leu4Ile missense_variant 0.29
pepQ 2860018 p.Val134Ala missense_variant 0.2
pepQ 2860396 p.Asp8Gly missense_variant 0.12
ribD 2987480 c.642G>C synonymous_variant 0.25
Rv2752c 3064516 c.1676A>G splice_region_variant&stop_retained_variant 0.15
Rv2752c 3064876 p.Ser439Tyr missense_variant 0.4
Rv2752c 3065205 c.987T>C synonymous_variant 0.4
thyX 3068101 c.-156G>T upstream_gene_variant 0.29
thyA 3073748 p.Thr242Ala missense_variant 0.2
thyA 3074160 c.311delC frameshift_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449068 p.Ala189Thr missense_variant 0.25
Rv3083 3449726 p.Arg408Gln missense_variant 0.33
Rv3083 3449787 c.1284C>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568420 p.Arg87Leu missense_variant 0.5
whiB7 3568580 p.Ala34Thr missense_variant 0.29
Rv3236c 3613307 c.-191G>T upstream_gene_variant 0.4
fbiA 3640999 p.His153Asp missense_variant 0.11
fbiB 3641545 p.Pro4Leu missense_variant 0.5
fbiB 3642625 p.Ala364Asp missense_variant 0.29
alr 3840778 p.Phe215Leu missense_variant 0.25
alr 3841170 p.Ala84Asp missense_variant 0.22
alr 3841349 c.72C>T synonymous_variant 0.14
rpoA 3877504 p.Ala335Glu missense_variant 0.33
rpoA 3877607 p.Leu301Met missense_variant 0.25
rpoA 3878249 p.Ser87Thr missense_variant 0.4
clpC1 4038253 p.Phe818Leu missense_variant 0.5
clpC1 4038587 c.2118C>A synonymous_variant 0.33
clpC1 4038720 p.Leu662Gln missense_variant 0.25
clpC1 4038747 p.Arg653Leu missense_variant 0.29
clpC1 4039778 c.927A>G synonymous_variant 0.25
clpC1 4040300 c.405C>A synonymous_variant 0.4
clpC1 4040414 c.291G>A synonymous_variant 0.15
embC 4241071 c.1209C>T synonymous_variant 0.25
embC 4241572 c.1710C>T synonymous_variant 1.0
embC 4241580 p.Ile573Ser missense_variant 0.25
embC 4242506 p.Leu882Met missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243010 p.Lys1050Glu missense_variant 0.15
embA 4243126 c.-107G>T upstream_gene_variant 0.18
embA 4243209 c.-24C>T upstream_gene_variant 0.15
embA 4243833 p.Ala201Thr missense_variant 1.0
embA 4245334 p.Glu701Val missense_variant 0.33
embA 4246426 p.Pro1065Leu missense_variant 0.17
embA 4246506 p.Ala1092Ser missense_variant 0.29
embB 4246533 p.Arg7Thr missense_variant 0.5
embB 4246599 p.Val29Glu missense_variant 0.5
embB 4246930 p.Gln139His missense_variant 1.0
embB 4248614 p.Ala701Thr missense_variant 0.13
embB 4248779 p.Glu756Lys missense_variant 0.4
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4268246 c.591G>T synonymous_variant 0.25
aftB 4268259 p.Gly193Val missense_variant 0.25
aftB 4268755 p.Ala28Ser missense_variant 0.67
ubiA 4268986 p.Val283Ala missense_variant 0.33
ethA 4326118 c.1356T>C synonymous_variant 0.25
ethR 4328121 p.Gln191His missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0