TB-Profiler result

Run: SRR12199469
Summary

Run ID: SRR12199469

Sample name:

Date: 03-04-2023 06:42:25

Number of reads: 567157

Percentage reads mapped: 97.83

Strain: lineage1.1.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8588 p.Glu429Asp missense_variant 1.0
gyrA 8657 c.1356C>A synonymous_variant 0.14
gyrA 8849 c.1548C>T synonymous_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9152 p.Tyr617* stop_gained 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490689 c.-94C>A upstream_gene_variant 0.22
fgd1 490751 c.-32T>G upstream_gene_variant 0.31
fgd1 491276 p.Val165Ala missense_variant 0.18
fgd1 491282 p.Asp167Val missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576091 c.744C>A synonymous_variant 0.18
mshA 576094 c.747G>A synonymous_variant 0.18
rpoB 761152 p.Leu449Gln missense_variant 0.18
rpoB 761770 p.Met655Thr missense_variant 1.0
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 764512 c.1143G>A synonymous_variant 0.22
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776163 p.Thr773Asn missense_variant 0.12
mmpL5 776567 p.Met638Ile missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.15
mmpL5 778246 p.Gly79Ser missense_variant 0.25
mmpR5 779167 p.Leu60Met missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801013 p.Gln69* stop_gained 0.14
rplC 801027 c.219C>A synonymous_variant 0.12
rplC 801067 p.Asp87Asn missense_variant 0.14
fbiC 1303097 p.Ala56Val missense_variant 0.15
fbiC 1303807 p.Gln293Lys missense_variant 0.25
fbiC 1304223 c.1293G>T synonymous_variant 0.22
fbiC 1304689 p.Arg587Trp missense_variant 0.17
fbiC 1304739 c.1809C>T synonymous_variant 0.13
fbiC 1304859 c.1929C>T synonymous_variant 0.13
fbiC 1305338 p.Gly803Asp missense_variant 0.12
Rv1258c 1406305 p.Gly346Ser missense_variant 0.13
Rv1258c 1406367 p.Tyr325Cys missense_variant 0.12
Rv1258c 1406740 p.His201Tyr missense_variant 0.15
Rv1258c 1407102 p.Ala80Val missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417173 p.Leu59Ile missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.13
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.16
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.16
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.13
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.14
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.14
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.12
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.13
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.12
rrl 1475091 n.1434G>A non_coding_transcript_exon_variant 0.12
rrl 1475092 n.1435A>C non_coding_transcript_exon_variant 0.12
rrl 1475094 n.1437C>T non_coding_transcript_exon_variant 0.13
rrl 1475108 n.1451C>G non_coding_transcript_exon_variant 0.11
rrl 1475115 n.1458A>C non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.15
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.19
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.18
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.26
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.26
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.25
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.29
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.32
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.31
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.2
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.17
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.21
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.2
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.18
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.18
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.2
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.18
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.19
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.18
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.16
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.18
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.19
fabG1 1673262 c.-178G>A upstream_gene_variant 0.12
inhA 1674234 c.33G>C synonymous_variant 0.15
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1918306 p.Arg123Cys missense_variant 0.18
ndh 2103022 c.21C>G synonymous_variant 1.0
ndh 2103202 c.-160C>A upstream_gene_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154783 c.1329T>C synonymous_variant 0.14
katG 2155822 p.His97Arg missense_variant 0.18
katG 2155929 c.183G>A synonymous_variant 0.18
PPE35 2167814 c.2799C>T synonymous_variant 0.13
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.16
PPE35 2170147 p.Ser156Ala missense_variant 0.4
PPE35 2170403 c.210C>G synonymous_variant 0.4
PPE35 2170406 c.207A>G synonymous_variant 0.4
PPE35 2170484 c.129C>A synonymous_variant 0.15
PPE35 2170533 p.Ala27Glu missense_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223144 p.Arg7Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223355 c.-191G>T upstream_gene_variant 0.17
pncA 2289063 p.Gly60Asp missense_variant 0.14
kasA 2518123 c.9G>A synonymous_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746397 p.Val401Asp missense_variant 0.29
pepQ 2859489 c.930C>A synonymous_variant 0.29
pepQ 2859826 p.Ala198Asp missense_variant 0.25
pepQ 2860180 p.Gly80Val missense_variant 0.18
ribD 2986941 p.Pro35Thr missense_variant 0.25
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3066276 c.-85G>A upstream_gene_variant 0.18
Rv2752c 3067017 c.-826G>T upstream_gene_variant 0.14
thyX 3067489 p.Lys153Glu missense_variant 0.33
thyX 3067964 c.-19C>A upstream_gene_variant 0.13
thyX 3067977 c.-32G>A upstream_gene_variant 0.13
thyA 3074051 p.Met141Val missense_variant 0.12
thyA 3074648 c.-177T>G upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087123 p.Ala102Ser missense_variant 0.12
ald 3087781 p.Val321Glu missense_variant 0.17
fbiD 3339339 c.222G>A synonymous_variant 0.17
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449395 p.Cys298Arg missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474356 p.Glu117Gly missense_variant 0.25
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612427 c.690G>A synonymous_variant 0.2
Rv3236c 3612759 p.Gly120Cys missense_variant 0.29
Rv3236c 3612766 c.351C>A synonymous_variant 0.25
fbiA 3640583 p.Arg14His missense_variant 0.14
fbiB 3641112 c.-423T>C upstream_gene_variant 0.18
fbiB 3641612 c.78C>A synonymous_variant 0.22
fbiB 3642754 c.1222delG frameshift_variant 0.18
alr 3840863 c.558C>T synonymous_variant 0.13
alr 3841127 c.294A>G synonymous_variant 0.25
alr 3841247 c.174C>T synonymous_variant 0.22
alr 3841546 c.-126C>A upstream_gene_variant 0.21
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038909 p.Pro599His missense_variant 0.12
clpC1 4039003 p.Asn568Asp missense_variant 0.25
clpC1 4039495 p.Asp404Asn missense_variant 0.14
clpC1 4039691 c.1014G>C synonymous_variant 0.2
clpC1 4039801 p.Ile302Val missense_variant 1.0
clpC1 4040001 p.His235Ala missense_variant 0.14
clpC1 4040010 p.Ala232Arg missense_variant 0.21
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044038 p.Gly82Trp missense_variant 0.18
embC 4239785 c.-77delT upstream_gene_variant 0.12
embC 4239888 p.Arg9Leu missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241527 c.1665C>T synonymous_variant 0.33
embC 4241632 c.1770C>T synonymous_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4244225 c.993C>G synonymous_variant 1.0
embA 4245510 p.Pro760Thr missense_variant 0.15
embB 4245587 c.-927G>A upstream_gene_variant 0.18
embA 4245777 p.Ala849Ser missense_variant 0.25
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247113 c.600G>T synonymous_variant 0.29
embB 4247470 c.957T>C synonymous_variant 0.18
embB 4247472 p.Phe320Tyr missense_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267044 p.Thr598Ile missense_variant 0.15
aftB 4267339 p.Leu500Phe missense_variant 1.0
aftB 4268012 c.825G>T synonymous_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327269 p.Trp69Arg missense_variant 0.12
whiB6 4338242 p.Gln94Glu missense_variant 1.0
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 4407873 c.330G>T synonymous_variant 1.0
gid 4408176 c.27T>C synonymous_variant 0.12