TB-Profiler result

Run: ERR245820
Summary

Run ID: ERR245820

Sample name:

Date: 31-03-2023 18:22:52

Number of reads: 1628027

Percentage reads mapped: 98.98

Strain: lineage1.1.3.2

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
lineage1 Indo-Oceanic EAI RD239 0.99
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.2 Indo-Oceanic NA RD239 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 5078 c.-162_-161insG upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7504 p.Arg68Pro missense_variant 0.23
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 1.0
gyrA 8377 p.Asp359Gly missense_variant 0.19
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.14
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
ccsA 620407 p.Pro173Ala missense_variant 0.27
rpoC 762836 c.-534C>G upstream_gene_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764751 p.Val461Gly missense_variant 0.32
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.95
mmpL5 777399 p.Thr361Arg missense_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417136 p.Ser71Ile missense_variant 0.44
atpE 1461019 c.-26C>A upstream_gene_variant 0.22
rrs 1471658 n.-188T>G upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.27
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.25
fabG1 1673449 p.Thr4Pro missense_variant 0.5
fabG1 1673546 p.Ala36Gly missense_variant 0.67
inhA 1674334 p.Arg45Gly missense_variant 0.23
inhA 1674883 p.Ile228Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102867 p.Ala59Val missense_variant 1.0
katG 2154615 c.1497G>C synonymous_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156073 c.39C>G synonymous_variant 0.24
katG 2156230 c.-119C>T upstream_gene_variant 0.3
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.33
PPE35 2169866 c.747G>C synonymous_variant 0.38
Rv1979c 2222231 p.Met312Val missense_variant 0.21
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222595 c.570G>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289293 c.-52C>G upstream_gene_variant 0.4
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.25
ahpC 2725954 c.-239C>T upstream_gene_variant 0.23
ahpC 2726051 c.-142G>A upstream_gene_variant 0.97
pepQ 2859381 c.1038C>G synonymous_variant 0.29
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064741 p.Gly484Ala missense_variant 0.3
Rv2752c 3064836 p.Leu452Phe missense_variant 0.29
Rv2752c 3065978 p.Asp72Tyr missense_variant 0.25
thyX 3067965 c.-20C>G upstream_gene_variant 0.4
thyA 3073817 p.Gln219Glu missense_variant 0.3
thyA 3073890 p.Leu194Phe missense_variant 0.47
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448353 c.-151T>G upstream_gene_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.16
Rv3083 3449673 p.Tyr390* stop_gained 0.3
Rv3083 3449731 p.Leu410Val missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3641271 p.Tyr243* stop_gained 0.5
fbiB 3641955 p.Gly141Arg missense_variant 0.25
fbiB 3642173 c.639G>A synonymous_variant 1.0
alr 3840456 p.Leu322Arg missense_variant 0.22
rpoA 3878580 c.-73A>C upstream_gene_variant 1.0
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.14
clpC1 4039363 p.Ala448Pro missense_variant 0.18
clpC1 4039932 p.Gly258Val missense_variant 0.31
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239870 p.Thr3Asn missense_variant 0.22
embC 4240646 p.Phe262Val missense_variant 0.5
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.29
embC 4241429 p.Phe523Val missense_variant 0.6
embC 4241456 p.Ala532Pro missense_variant 0.6
embC 4241556 p.Ser565Thr missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.8
embC 4242827 p.Leu989Val missense_variant 0.5
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244375 c.1143C>G synonymous_variant 0.5
embA 4245969 p.Pro913Ser missense_variant 0.94
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249504 p.Gln997His missense_variant 0.19
aftB 4268147 c.690C>G synonymous_variant 0.19
aftB 4268343 p.Arg165Pro missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.27
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4327912 p.Arg122Gly missense_variant 0.17
whiB6 4338493 p.Thr10Lys missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 0.97
gid 4407873 c.330G>T synonymous_variant 1.0