TB-Profiler result

Run: SRR6797525
Summary

Run ID: SRR6797525

Sample name:

Date: 04-04-2023 16:11:45

Number of reads: 690540

Percentage reads mapped: 99.32

Strain: lineage1.1.3.1

Drug-resistance: HR-TB

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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 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 Indo-Oceanic NA 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
gyrB 6647 p.Gly470Cys missense_variant 0.25 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
katG 2155795 p.Ala106Val missense_variant 0.2 isoniazid
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 5882 p.Gln215Lys missense_variant 0.15
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7996 p.Gly232Val missense_variant 0.29
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8577 p.Asp426Tyr missense_variant 0.14
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 576677 p.Ala444Ser missense_variant 0.13
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 764341 c.972G>T synonymous_variant 0.18
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 1.0
mmpS5 779641 c.-736C>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304984 p.Leu685Pro missense_variant 0.29
fbiC 1305367 p.Glu813* stop_gained 0.15
Rv1258c 1407386 c.-46C>A upstream_gene_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472439 n.594C>A non_coding_transcript_exon_variant 0.13
rrl 1475497 n.1840C>A non_coding_transcript_exon_variant 0.12
rrl 1476435 n.2778C>A non_coding_transcript_exon_variant 0.18
inhA 1674615 p.Met138Ile missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918136 p.Gly66Val missense_variant 0.13
ndh 2103171 c.-129G>T upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156158 c.-47A>T upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168314 p.Gln767* stop_gained 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223188 c.-24T>C upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.86
eis 2714304 c.1029C>A synonymous_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747117 p.Ala161Val missense_variant 0.33
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3067560 p.Arg129His missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087223 p.Glu135Gly missense_variant 0.11
fbiD 3339713 p.Arg199Leu missense_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449819 p.Leu439Pro missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475116 c.1110C>T synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568811 c.-132C>A upstream_gene_variant 0.14
Rv3236c 3612113 c.1003delG frameshift_variant 0.15
Rv3236c 3613127 c.-11G>T upstream_gene_variant 0.22
alr 3841253 c.168C>T synonymous_variant 1.0
ddn 3987089 c.246G>A synonymous_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242296 p.Asp812Tyr missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243033 p.Trp1057Cys missense_variant 0.12
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247025 p.Pro171Gln missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248982 p.Ser823Arg missense_variant 0.11
aftB 4267020 p.Pro606Gln missense_variant 0.14
aftB 4267070 c.1767C>A synonymous_variant 0.13
aftB 4268952 c.-116G>T upstream_gene_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338263 p.Ala87Ser missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0