TB-Profiler result

Run: SRR4035759

Summary

Run ID: SRR4035759

Sample name:

Date: 04-04-2023 07:16:52

Number of reads: 1376930

Percentage reads mapped: 99.43

Strain: lineage4.1.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 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 5089 c.-151A>G upstream_gene_variant 0.11
gyrB 6846 p.Asp536Gly missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8685 p.Ile462Val missense_variant 0.12
gyrA 8769 p.His490Tyr missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9442 p.Leu714Pro missense_variant 0.12
gyrA 9501 p.Arg734Gly missense_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491616 p.Glu278Asp missense_variant 0.13
mshA 575673 p.Val109Glu missense_variant 0.12
mshA 576392 p.Pro349Thr missense_variant 0.14
ccsA 620177 p.Val96Glu missense_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761465 c.1659G>A synonymous_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766403 p.Met1012Val missense_variant 0.13
rpoC 766629 p.Arg1087Gln missense_variant 0.13
rpoC 766661 p.Val1098Met missense_variant 0.14
rpoC 766692 p.Gly1108Ala missense_variant 0.12
rpoC 767129 p.Ile1254Val missense_variant 0.1
rpoC 767231 p.Tyr1288Asn missense_variant 0.12
mmpL5 775597 p.Ala962Pro missense_variant 0.15
mmpL5 775613 c.2868A>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776312 c.2169A>G synonymous_variant 0.12
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777681 p.Val267Ala missense_variant 0.14
mmpS5 778755 p.Phe51Leu missense_variant 0.12
mmpL5 779295 c.-815A>T upstream_gene_variant 0.22
mmpR5 779302 p.Arg105Cys missense_variant 0.22
mmpL5 779436 c.-956G>C upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800927 p.Arg40His missense_variant 0.17
rplC 801236 c.430delG frameshift_variant 0.17
rplC 801263 p.Gly152Asp missense_variant 0.13
rplC 801271 p.Ala155Ser missense_variant 0.14
fbiC 1303977 c.1047C>A synonymous_variant 0.14
fbiC 1304267 p.Arg446Gln missense_variant 0.18
fbiC 1304513 p.Val528Asp missense_variant 0.15
fbiC 1304523 c.1593G>C synonymous_variant 0.12
fbiC 1305060 p.Tyr710* stop_gained 0.13
fbiC 1305410 p.Ala827Val missense_variant 0.13
Rv1258c 1407169 p.Ala58Thr missense_variant 0.17
embR 1416522 p.Val276Leu missense_variant 0.13
embR 1416757 c.591G>C synonymous_variant 0.18
embR 1416768 p.Leu194Phe missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673201 c.-239G>A upstream_gene_variant 0.12
rpsA 1833420 c.-122C>T upstream_gene_variant 0.12
rpsA 1833596 p.Ser19Gly missense_variant 0.11
rpsA 1834175 p.Arg212Gly missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102108 p.Pro312Arg missense_variant 0.15
ndh 2102154 p.Leu297Val missense_variant 0.1
katG 2154843 c.1269T>C synonymous_variant 0.12
PPE35 2169979 p.Val212Ile missense_variant 0.14
PPE35 2170099 c.514C>T synonymous_variant 0.13
Rv1979c 2223056 p.Gly37Arg missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289703 c.-462G>C upstream_gene_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 0.97
eis 2715183 c.150T>C synonymous_variant 0.12
eis 2715557 c.-226delA upstream_gene_variant 0.17
folC 2747412 p.Ser63Gly missense_variant 0.12
folC 2747419 c.180C>G synonymous_variant 0.12
folC 2747604 c.-6G>T upstream_gene_variant 0.13
folC 2747753 c.-155G>C upstream_gene_variant 0.11
ribD 2987469 c.631C>T synonymous_variant 0.12
ribD 2987480 c.642G>A synonymous_variant 0.15
Rv2752c 3065240 p.Met318Leu missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339449 p.Val111Ala missense_variant 0.17
Rv3083 3448382 c.-122G>C upstream_gene_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475296 p.Glu430Asp missense_variant 0.18
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612086 p.Ala344Gly missense_variant 0.14
Rv3236c 3612523 c.594G>T synonymous_variant 0.25
Rv3236c 3613283 c.-167T>C upstream_gene_variant 0.11
alr 3840494 c.927G>T synonymous_variant 0.18
alr 3841079 c.342T>C synonymous_variant 0.12
rpoA 3877598 c.910C>T synonymous_variant 0.12
ddn 3986692 c.-152G>A upstream_gene_variant 0.15
ddn 3986751 c.-93C>G upstream_gene_variant 0.15
ddn 3986984 c.141G>A synonymous_variant 0.13
clpC1 4040198 p.Leu169Phe missense_variant 0.11
clpC1 4040765 c.-61G>T upstream_gene_variant 0.14
panD 4044330 c.-49A>G upstream_gene_variant 0.14
embC 4239851 c.-12G>T upstream_gene_variant 0.12
embC 4239974 c.112C>T synonymous_variant 0.22
embC 4242048 p.Ser729Phe missense_variant 0.13
embC 4242425 p.Arg855Gly missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246942 c.429G>A synonymous_variant 0.15
embB 4247523 p.Leu337Gln missense_variant 0.29
embB 4247942 p.Pro477Thr missense_variant 0.15
aftB 4267727 p.Trp370* stop_gained 0.13
aftB 4268227 p.Ala204Pro missense_variant 0.14
aftB 4268488 p.Met117Val missense_variant 0.12
ubiA 4269138 p.Cys232Trp missense_variant 0.12
ethA 4327627 c.-154G>A upstream_gene_variant 0.12
whiB6 4338457 p.Thr22Arg missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338608 c.-87G>C upstream_gene_variant 0.13
gid 4408164 c.39A>T synonymous_variant 0.14