TB-Profiler result

Run: SRR21677876

Summary

Run ID: SRR21677876

Sample name:

Date: 04-04-2023 02:49:13

Number of reads: 225732

Percentage reads mapped: 96.41

Strain: lineage4.1

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 Euro-American T;X;H 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7376 c.75G>A synonymous_variant 0.33
gyrA 7472 c.171T>C synonymous_variant 0.29
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8775 p.Asp492Asn missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759967 p.Ser54Leu missense_variant 0.25
rpoB 760270 p.Thr155Ile missense_variant 0.12
rpoB 760951 p.Gln382Pro missense_variant 0.33
rpoB 761484 p.Gly560Cys missense_variant 0.17
rpoB 762875 p.Tyr1023* stop_gained 0.22
rpoC 763559 p.Lys64Glu missense_variant 0.5
rpoC 763731 p.Ala121Val missense_variant 0.29
rpoC 764270 p.Ala301Ser missense_variant 0.17
rpoC 764529 p.Arg387His missense_variant 0.25
rpoC 764564 p.Leu399Ile missense_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765467 p.Leu700Val missense_variant 0.2
rpoC 766388 p.Gly1007Ser missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775823 c.2658G>A synonymous_variant 0.29
mmpL5 776409 p.Leu691Pro missense_variant 0.2
mmpL5 776868 p.Arg538Gln missense_variant 0.14
mmpL5 776899 p.Asp528Asn missense_variant 0.12
mmpL5 777578 c.903C>A synonymous_variant 0.17
mmpL5 777728 c.753T>C synonymous_variant 0.13
mmpR5 779130 c.144delC frameshift_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781663 p.Thr35Ile missense_variant 0.2
rplC 801280 p.Ala158Ser missense_variant 0.13
rplC 801288 c.480G>T synonymous_variant 0.12
fbiC 1302814 c.-117C>T upstream_gene_variant 1.0
fbiC 1303731 c.801A>G synonymous_variant 0.29
fbiC 1304415 c.1485G>T synonymous_variant 0.13
fbiC 1304502 c.1572G>A synonymous_variant 0.15
fbiC 1304826 c.1900delT frameshift_variant 0.17
fbiC 1305010 p.Val694Met missense_variant 0.29
Rv1258c 1406539 p.Ala268Thr missense_variant 0.25
embR 1416996 p.Glu118* stop_gained 0.22
embR 1417096 c.252T>A synonymous_variant 0.15
embR 1417537 c.-190T>G upstream_gene_variant 0.22
atpE 1461259 p.Ala72Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472206 n.361G>A non_coding_transcript_exon_variant 0.33
rrs 1472508 n.663T>A non_coding_transcript_exon_variant 0.14
rrl 1474892 n.1235G>C non_coding_transcript_exon_variant 0.5
rrl 1475327 n.1670G>A non_coding_transcript_exon_variant 0.4
fabG1 1673243 c.-197G>T upstream_gene_variant 0.2
fabG1 1673519 p.Ile27Thr missense_variant 0.33
inhA 1674289 p.Gln30Lys missense_variant 0.33
rpsA 1833460 c.-82G>T upstream_gene_variant 0.2
rpsA 1833928 c.387G>A synonymous_variant 0.13
rpsA 1834306 c.765T>C synonymous_variant 0.12
rpsA 1834449 p.Lys303Met missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918625 p.Pro229Gln missense_variant 0.12
katG 2155447 p.Ala222Val missense_variant 0.4
katG 2156066 p.Ala16Pro missense_variant 0.2
PPE35 2168473 c.2139dupC frameshift_variant 0.2
PPE35 2168778 p.Thr612Ile missense_variant 0.22
Rv1979c 2221943 p.Arg408Trp missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289948 c.-707C>T upstream_gene_variant 0.22
kasA 2518165 c.51C>T synonymous_variant 0.15
eis 2715024 c.309A>G synonymous_variant 0.17
eis 2715164 p.Glu57* stop_gained 0.29
ahpC 2726055 c.-138G>C upstream_gene_variant 0.18
ahpC 2726766 p.Lys192Glu missense_variant 0.14
folC 2746366 c.1233G>A synonymous_variant 0.13
folC 2747290 c.309A>T synonymous_variant 0.17
pepQ 2859801 c.618G>A synonymous_variant 0.13
pepQ 2860154 p.Glu89Gln missense_variant 0.2
Rv2752c 3064875 c.1317C>T synonymous_variant 0.18
Rv2752c 3065394 p.Met266Ile missense_variant 0.18
thyX 3067838 c.108C>T synonymous_variant 0.5
thyX 3068082 c.-137T>C upstream_gene_variant 0.2
thyA 3073766 p.Asp236Tyr missense_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087311 c.492C>A synonymous_variant 0.17
Rv3083 3448436 c.-68T>A upstream_gene_variant 0.33
Rv3083 3448511 c.9_13dupGCATT frameshift_variant 0.29
Rv3083 3448731 c.228C>T synonymous_variant 0.22
Rv3083 3449595 c.1092A>G synonymous_variant 0.33
Rv3083 3449787 c.1284C>T synonymous_variant 1.0
Rv3083 3449902 p.Glu467Lys missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568595 p.Phe29Leu missense_variant 0.5
Rv3236c 3612121 c.996C>T synonymous_variant 0.29
Rv3236c 3612177 c.940C>A synonymous_variant 0.25
Rv3236c 3612663 c.454C>T synonymous_variant 0.25
Rv3236c 3612933 p.Ala62Ser missense_variant 0.18
fbiA 3640389 c.-154C>T upstream_gene_variant 0.17
fbiB 3641776 p.Glu81Val missense_variant 0.33
fbiB 3642194 c.660C>T synonymous_variant 0.22
fbiB 3642484 c.952_953delCG frameshift_variant 0.33
alr 3840417 p.Cys335Tyr missense_variant 0.18
alr 3840660 p.Gly254Asp missense_variant 0.15
ddn 3986675 c.-169G>T upstream_gene_variant 0.17
ddn 3986744 c.-100C>A upstream_gene_variant 0.67
clpC1 4038761 c.1944C>A synonymous_variant 0.22
clpC1 4038822 p.Glu628Gly missense_variant 0.22
clpC1 4039083 p.Asp541Gly missense_variant 0.33
clpC1 4039385 c.1320C>T synonymous_variant 0.4
clpC1 4040542 p.Ser55Ala missense_variant 0.15
panD 4043877 c.405G>A synonymous_variant 0.22
panD 4044065 p.Gly73Arg missense_variant 0.2
panD 4044133 p.Asp50Ala missense_variant 0.29
panD 4044237 c.45G>A synonymous_variant 0.12
panD 4044380 c.-99C>T upstream_gene_variant 0.15
embC 4239680 c.-183C>T upstream_gene_variant 0.22
embC 4240461 p.Val200Ala missense_variant 0.29
embC 4241572 c.1710C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243833 p.Ala201Thr missense_variant 1.0
embA 4244295 p.Ala355Ser missense_variant 0.29
embB 4246930 p.Gln139His missense_variant 1.0
embB 4247491 c.978G>T synonymous_variant 1.0
embB 4248568 p.Trp685Cys missense_variant 0.14
embB 4249136 p.Val875Phe missense_variant 0.17
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267985 c.852C>T synonymous_variant 0.33
aftB 4268063 c.774G>A synonymous_variant 0.13
aftB 4268455 p.Val128Leu missense_variant 0.22
ethA 4326123 p.Ser451Thr missense_variant 0.12
ethA 4327374 p.Ile34Val missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0