TB-Profiler result

Run: SRR4035710
Summary

Run ID: SRR4035710

Sample name:

Date: 04-04-2023 07:15:05

Number of reads: 1154500

Percentage reads mapped: 99.49

Strain: lineage4.1.2

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 0.99
lineage4.1.2 Euro-American T;H None 0.99
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 6082 c.843G>A synonymous_variant 0.14
gyrB 6092 p.His285Tyr missense_variant 0.14
gyrB 6140 p.Val301Met missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7863 p.Asn188Asp missense_variant 0.11
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8761 p.Val487Ala missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491729 p.Asp316Gly missense_variant 0.18
ccsA 619707 c.-184T>C upstream_gene_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760595 c.789C>G synonymous_variant 0.1
rpoB 761427 p.Pro541Ser missense_variant 0.12
rpoB 761431 p.Ile542Asn missense_variant 0.14
rpoB 762098 c.2292C>T synonymous_variant 0.13
rpoB 762506 p.Phe900Leu missense_variant 0.1
rpoB 763090 p.Lys1095Thr missense_variant 0.15
rpoB 763121 c.3316delA frameshift_variant 0.15
rpoC 763353 c.-17_-16insG upstream_gene_variant 0.13
rpoC 763525 c.156C>T synonymous_variant 0.13
rpoC 763552 c.183C>T synonymous_variant 0.14
rpoC 764223 c.858dupG frameshift_variant 0.15
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766029 p.Arg887Leu missense_variant 0.13
rpoC 766373 p.Ser1002Pro missense_variant 0.11
rpoC 766494 p.Gly1042Asp missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303615 c.688delC frameshift_variant 0.11
fbiC 1303648 p.Val240Met missense_variant 0.12
fbiC 1303655 p.Leu242Pro missense_variant 0.14
fbiC 1303664 p.Leu245Pro missense_variant 0.2
embR 1416758 p.Leu197Pro missense_variant 0.25
atpE 1461166 p.Arg41Pro missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471889 n.44G>A non_coding_transcript_exon_variant 0.14
rrs 1472785 n.940G>A non_coding_transcript_exon_variant 0.15
rrl 1474078 n.421_422insA non_coding_transcript_exon_variant 0.5
rrl 1474290 n.633T>C non_coding_transcript_exon_variant 0.18
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.15
rrl 1474566 n.909G>A non_coding_transcript_exon_variant 0.17
rrl 1476126 n.2469C>T non_coding_transcript_exon_variant 0.14
rrl 1476261 n.2604A>T non_coding_transcript_exon_variant 0.13
fabG1 1673999 p.Asp187Gly missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102575 p.Glu156Asp missense_variant 0.13
katG 2154513 c.1599G>T synonymous_variant 0.13
katG 2154805 p.Leu436Pro missense_variant 0.1
katG 2155412 p.Gly234Trp missense_variant 0.13
katG 2155782 c.330C>A synonymous_variant 0.18
katG 2155790 p.His108Asn missense_variant 0.17
Rv1979c 2223107 p.Val20Leu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288819 p.Gln141His missense_variant 0.12
pncA 2289925 c.-684T>A upstream_gene_variant 0.18
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714735 c.598C>T synonymous_variant 0.12
eis 2714763 c.570G>C synonymous_variant 0.12
ahpC 2726204 c.12A>C synonymous_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.27
ahpC 2726610 p.Pro140Ala missense_variant 0.11
ahpC 2726765 c.575dupA frameshift_variant 0.2
folC 2746895 p.Gly235Ala missense_variant 0.11
folC 2747203 c.396G>C synonymous_variant 0.11
folC 2747621 c.-23A>G upstream_gene_variant 0.12
thyA 3073878 p.Glu198Asp missense_variant 0.15
thyA 3073883 p.Gly197Ser missense_variant 0.14
thyA 3073894 p.Gly193Asp missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339652 p.Thr179Ala missense_variant 0.11
Rv3083 3448589 p.Asp29Val missense_variant 0.12
Rv3083 3448968 c.465C>G synonymous_variant 0.13
Rv3083 3449332 p.Leu277Phe missense_variant 0.14
Rv3083 3449397 p.Cys298Trp missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474317 p.Val104Asp missense_variant 0.14
fprA 3474332 c.327delT frameshift_variant 0.15
fprA 3474546 c.540T>C synonymous_variant 0.11
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
alr 3841130 c.291G>T synonymous_variant 0.12
rpoA 3877948 p.Thr187Ile missense_variant 0.13
panD 4043878 c.403delC frameshift_variant 0.12
embC 4239983 p.Ala41Ser missense_variant 0.17
embC 4239988 c.126G>A synonymous_variant 0.18
embC 4240191 p.Pro110Leu missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244077 p.Arg282Leu missense_variant 0.17
embB 4245566 c.-948C>T upstream_gene_variant 0.13
embB 4246592 p.Arg27Cys missense_variant 0.22
embB 4247830 c.1317A>T synonymous_variant 0.18
embB 4247838 p.Leu442Pro missense_variant 0.11
embB 4249411 c.2898G>C synonymous_variant 0.13
embB 4249415 p.Val968Ile missense_variant 0.13
embB 4249462 c.2949G>T synonymous_variant 0.15
aftB 4267124 c.1713T>C synonymous_variant 0.12
aftB 4267143 p.Ala565Val missense_variant 0.14
aftB 4268504 c.333G>A synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0