TB-Profiler result

Run: SRR11972241
Summary

Run ID: SRR11972241

Sample name:

Date: 03-04-2023 05:33:11

Number of reads: 197333

Percentage reads mapped: 99.18

Strain:

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 0.96
lineage1.2.2.2 Indo-Oceanic NA RD239 0.95
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 5075 c.-165C>T upstream_gene_variant 0.95
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6233 p.Ala332Ser missense_variant 0.2
gyrB 7036 p.Lys599Asn missense_variant 0.12
gyrB 7160 p.Ala641Ser missense_variant 0.22
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 8805 p.Asp502Tyr missense_variant 0.14
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9247 p.Val649Glu missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490680 c.-103A>G upstream_gene_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575520 p.Ala58Val missense_variant 0.4
mshA 575907 p.Ala187Val missense_variant 0.23
mshA 576695 p.Ala450Thr missense_variant 0.29
mshA 576784 c.1437C>T synonymous_variant 0.22
ccsA 620251 p.Gly121Arg missense_variant 0.17
rpoB 759947 c.141C>A synonymous_variant 0.75
rpoB 760596 p.Thr264Ser missense_variant 0.25
rpoB 760971 p.Arg389Trp missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763599 p.Arg77His missense_variant 0.25
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764831 p.Glu488Lys missense_variant 0.22
rpoC 764933 p.Ile522Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777360 p.Ala374Val missense_variant 0.2
mmpR5 779192 p.Ser68Asn missense_variant 0.33
mmpR5 779407 p.Arg140Trp missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801266 p.Gly153Glu missense_variant 0.12
fbiC 1302903 c.-28T>C upstream_gene_variant 1.0
fbiC 1304145 p.Trp405* stop_gained 0.25
fbiC 1305206 p.Pro759His missense_variant 0.22
Rv1258c 1406618 c.723G>T synonymous_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 0.22
Rv1258c 1407157 p.Ala62Thr missense_variant 1.0
embR 1416537 p.Ala271Thr missense_variant 0.13
embR 1416552 p.Ala266Thr missense_variant 0.13
embR 1416812 p.Glu179Gly missense_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417491 c.-144C>T upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473453 n.-205G>T upstream_gene_variant 0.15
rrl 1475470 n.1813T>A non_coding_transcript_exon_variant 0.29
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.18
tlyA 1917904 c.-36C>T upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102728 c.315T>G synonymous_variant 1.0
katG 2154177 c.1935G>A synonymous_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156568 c.-457G>T upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.94
PPE35 2170524 p.Ala30Val missense_variant 0.22
Rv1979c 2222110 p.Ser352Phe missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222602 c.562delC frameshift_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288744 p.Asp166Glu missense_variant 0.22
pncA 2289619 c.-378T>A upstream_gene_variant 0.29
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714654 c.679C>A synonymous_variant 0.4
ahpC 2726051 c.-142G>A upstream_gene_variant 0.83
folC 2747779 c.-181G>A upstream_gene_variant 0.33
ribD 2987061 p.Arg75Cys missense_variant 0.25
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
thyA 3074059 p.Ile138Thr missense_variant 0.33
thyA 3074402 p.Thr24Ser missense_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086808 c.-12A>G upstream_gene_variant 0.17
fbiD 3339069 c.-49C>T upstream_gene_variant 0.22
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449799 c.1296C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.9
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3640372 c.-171A>G upstream_gene_variant 0.19
fbiA 3640553 p.Thr4Ile missense_variant 0.29
fbiA 3640739 p.Met66Thr missense_variant 0.2
fbiB 3640842 c.-693C>T upstream_gene_variant 0.29
alr 3840644 c.777G>T synonymous_variant 0.18
alr 3841534 c.-114C>T upstream_gene_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 1.0
alr 3841568 c.-148G>A upstream_gene_variant 1.0
alr 3841570 c.-151delA upstream_gene_variant 1.0
alr 3841574 c.-154T>G upstream_gene_variant 1.0
alr 3841578 c.-158G>T upstream_gene_variant 1.0
alr 3841582 c.-162A>G upstream_gene_variant 1.0
alr 3841584 c.-164C>A upstream_gene_variant 1.0
alr 3841589 c.-170delG upstream_gene_variant 1.0
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0
rpoA 3878254 p.Val85Ala missense_variant 0.2
ddn 3986729 c.-115T>C upstream_gene_variant 0.17
ddn 3986841 c.-3G>T upstream_gene_variant 0.15
ddn 3987100 p.Pro86Leu missense_variant 0.14
clpC1 4039484 c.1221T>C synonymous_variant 0.33
clpC1 4039614 p.Asp364Gly missense_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040621 c.84C>A synonymous_variant 0.93
clpC1 4040694 p.Arg4Leu missense_variant 0.14
embC 4240387 c.525C>A synonymous_variant 0.83
embC 4240671 p.Thr270Ile missense_variant 0.6
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241404 p.Asp514Glu missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242682 c.-551C>A upstream_gene_variant 0.29
embA 4243312 p.Leu27Gln missense_variant 0.25
embA 4244175 p.Ala315Pro missense_variant 0.2
embA 4244291 c.1059G>A synonymous_variant 0.14
embA 4244522 c.1290C>G synonymous_variant 0.13
embA 4244897 c.1665T>C synonymous_variant 0.14
embA 4245106 p.Phe625Ser missense_variant 0.29
embA 4245444 p.Asp738Tyr missense_variant 0.25
embB 4247646 p.Glu378Ala missense_variant 0.83
aftB 4268893 c.-57C>A upstream_gene_variant 0.67
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327827 c.-354A>G upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0