TB-Profiler result

Run: SRR5818675
Summary

Run ID: SRR5818675

Sample name:

Date: 04-04-2023 11:42:53

Number of reads: 1434232

Percentage reads mapped: 99.24

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrB 6666 p.Gln476Leu missense_variant 0.12
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 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
gyrA 9580 p.Gly760Asp missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoB 759756 c.-51C>T upstream_gene_variant 0.12
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.14
rpoB 762574 c.2770delC frameshift_variant 0.25
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 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 777525 p.Gly319Val missense_variant 0.12
mmpL5 777992 p.Asn163Lys missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781422 c.-138A>G upstream_gene_variant 0.11
Rv1258c 1407247 p.Trp32Arg missense_variant 0.17
Rv1258c 1407518 c.-178C>G upstream_gene_variant 0.12
embR 1416774 c.573delC frameshift_variant 0.17
embR 1416989 c.358delA frameshift_variant 0.18
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474084 n.431delA non_coding_transcript_exon_variant 0.29
rrl 1475637 n.1980T>A non_coding_transcript_exon_variant 0.12
rrl 1476058 n.2401T>C non_coding_transcript_exon_variant 0.2
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102074 p.Met323Lys missense_variant 0.14
katG 2153970 p.Asp714Glu missense_variant 0.24
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156149 c.-38A>T upstream_gene_variant 0.11
PPE35 2167883 c.2730C>A synonymous_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168052 p.Val854Ala missense_variant 0.13
PPE35 2168863 c.1750C>T synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.6
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.12
kasA 2518609 p.Met165Ile missense_variant 0.14
kasA 2519344 c.1230G>T synonymous_variant 0.22
eis 2715436 c.-104G>A upstream_gene_variant 0.12
eis 2715440 c.-108A>C upstream_gene_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087634 p.Gly272Val missense_variant 0.24
ald 3087639 p.Cys274Ser missense_variant 0.22
Rv3083 3448714 p.Asp71His missense_variant 1.0
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
Rv3236c 3613201 c.-85C>T upstream_gene_variant 0.2
alr 3840713 c.708C>T synonymous_variant 0.96
rpoA 3878497 p.Ser4* stop_gained 0.18
ddn 3987057 p.Arg72Trp missense_variant 0.96
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243790 c.558G>A synonymous_variant 0.4
embA 4243848 p.Val206Met missense_variant 1.0
embB 4245902 c.-612G>A upstream_gene_variant 0.14
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.31
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4328212 c.-740delC upstream_gene_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