TB-Profiler result

Run: SRR6797439
Summary

Run ID: SRR6797439

Sample name:

Date: 04-04-2023 16:09:42

Number of reads: 375561

Percentage reads mapped: 98.76

Strain: lineage1.1

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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.98
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 5041 c.-199G>T upstream_gene_variant 0.25
gyrB 5762 p.Ala175Thr missense_variant 0.25
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 0.75
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7714 p.Ala138Val missense_variant 0.33
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
fgd1 491027 p.Asn82Thr missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575664 p.Gly106Ala missense_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 0.75
ccsA 620425 p.Val179Ile missense_variant 0.5
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764232 p.Lys288Met missense_variant 0.5
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781427 c.-133G>A upstream_gene_variant 0.67
fbiC 1304106 c.1176G>A synonymous_variant 0.25
embR 1416475 p.Tyr291* stop_gained 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474015 n.358T>A non_coding_transcript_exon_variant 0.67
rrl 1476086 n.2429G>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168132 p.Asp827Glu missense_variant 0.25
PPE35 2168222 c.2391G>T synonymous_variant 0.25
PPE35 2169092 c.1521G>T synonymous_variant 0.33
PPE35 2169369 p.Gly415Ala missense_variant 0.67
PPE35 2169604 p.Gly337Cys missense_variant 0.25
PPE35 2169671 c.942C>T synonymous_variant 0.12
PPE35 2170291 p.Ala108Ser missense_variant 0.22
Rv1979c 2221791 c.1374G>T synonymous_variant 0.14
Rv1979c 2222282 p.Ile295Val missense_variant 0.43
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222484 c.681C>G synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289557 c.-316C>A upstream_gene_variant 0.18
pncA 2289585 c.-344C>T upstream_gene_variant 0.2
pncA 2290199 c.-958C>G upstream_gene_variant 0.67
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2860418 p.Val1Met missense_variant 0.15
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087113 c.294C>A synonymous_variant 0.17
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
alr 3840632 c.789A>T synonymous_variant 0.17
alr 3841253 c.168C>T synonymous_variant 0.43
rpoA 3878306 p.Gly68Trp missense_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044421 c.-140G>T upstream_gene_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240926 p.Cys355Phe missense_variant 0.67
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244840 c.1608G>A synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246290 p.Leu1020Ile missense_variant 0.18
embB 4246343 c.-171G>C upstream_gene_variant 0.22
embA 4246458 p.Glu1076* stop_gained 0.22
embB 4246771 c.258C>T synonymous_variant 0.4
embB 4247261 p.Gln250Lys missense_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268702 p.Asn45Lys missense_variant 0.71
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326007 c.1467T>C synonymous_variant 0.62
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0