TB-Profiler result

Run: ERR2229403
Summary

Run ID: ERR2229403

Sample name:

Date: 31-03-2023 17:09:40

Number of reads: 726575

Percentage reads mapped: 98.71

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 6020 p.Val261Met missense_variant 0.12
gyrB 7183 p.Phe648Leu missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7522 p.Ala74Asp missense_variant 0.13
gyrA 7805 c.504C>T synonymous_variant 0.25
gyrA 8809 p.Gly503Val missense_variant 0.13
gyrA 9286 p.Ala662Val missense_variant 0.25
fgd1 490749 c.-34G>T upstream_gene_variant 0.17
fgd1 490818 c.36C>T synonymous_variant 0.13
mshA 575207 c.-141A>G upstream_gene_variant 0.25
mshA 576108 p.Ala254Gly missense_variant 0.25
ccsA 619883 c.-8G>A upstream_gene_variant 0.33
ccsA 620278 p.Arg130Ser missense_variant 0.33
ccsA 620846 p.Ser319Trp missense_variant 0.22
rpoB 761152 p.Leu449Gln missense_variant 0.38
rpoB 761259 p.Gly485Trp missense_variant 0.15
rpoB 762178 p.Arg791Leu missense_variant 0.17
rpoC 765225 p.Ile619Asn missense_variant 0.18
rpoC 765354 p.Trp662* stop_gained 0.18
rpoC 765391 c.2022C>T synonymous_variant 0.18
rpoC 765779 p.Asp804Tyr missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776008 p.His825Asp missense_variant 0.2
mmpL5 776009 c.2472A>G synonymous_variant 0.2
mmpL5 776017 p.Ile822Val missense_variant 0.18
mmpL5 776022 p.Val820Ala missense_variant 0.18
mmpL5 776026 p.Ser819Pro missense_variant 0.18
mmpL5 776031 p.Gly817Val missense_variant 0.18
mmpL5 777119 p.His454Gln missense_variant 0.3
mmpL5 777122 c.1359C>T synonymous_variant 0.3
mmpL5 777128 c.1353A>G synonymous_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800935 p.Glu43Lys missense_variant 0.18
rplC 801114 c.306C>G synonymous_variant 0.22
fbiC 1303194 c.264C>T synonymous_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406435 c.906G>T synonymous_variant 0.29
embR 1416907 c.441G>T synonymous_variant 0.12
embR 1417253 p.Thr32Asn missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474627 n.970G>T non_coding_transcript_exon_variant 0.67
rrl 1475812 n.2155T>A non_coding_transcript_exon_variant 0.33
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
fabG1 1673895 p.Asn152Lys missense_variant 0.5
rpsA 1834088 p.Val183Leu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101912 c.1131G>A synonymous_variant 0.14
ndh 2102367 p.Ala226Pro missense_variant 0.18
ndh 2102368 c.675C>T synonymous_variant 0.18
ndh 2102446 c.597C>A synonymous_variant 0.13
ndh 2102875 c.168C>T synonymous_variant 0.15
katG 2153975 p.Ala713Ser missense_variant 0.18
katG 2154710 p.Thr468Ser missense_variant 0.15
katG 2155306 p.Gly269Val missense_variant 0.12
PPE35 2167814 c.2799C>T synonymous_variant 0.14
PPE35 2167995 p.Ser873Asn missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169091 p.Val508Leu missense_variant 0.18
PPE35 2169209 c.1404C>G synonymous_variant 0.18
PPE35 2169217 p.Glu466Gln missense_variant 0.18
PPE35 2169352 p.Ala421Thr missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.61
Rv1979c 2222083 p.Leu361His missense_variant 0.2
Rv1979c 2223002 p.Gly55Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288986 p.Asp86Tyr missense_variant 0.15
kasA 2518801 c.687G>A synonymous_variant 0.2
kasA 2518809 p.Lys232Arg missense_variant 0.15
kasA 2518873 c.759C>T synonymous_variant 0.12
kasA 2518879 c.765A>G synonymous_variant 0.12
eis 2714728 p.Ala202Glu missense_variant 0.22
ribD 2987031 p.Pro65Thr missense_variant 0.67
Rv2752c 3065930 p.Gly88Trp missense_variant 0.13
thyX 3067300 p.Leu216Val missense_variant 0.2
thyX 3067550 c.396G>T synonymous_variant 0.14
thyX 3067983 c.-38G>A upstream_gene_variant 0.18
fprA 3474587 p.Val194Ala missense_variant 0.2
fprA 3474730 p.Gly242Ser missense_variant 0.5
Rv3236c 3612966 p.Val51Leu missense_variant 0.17
fbiA 3640357 c.-186G>A upstream_gene_variant 0.12
fbiA 3640745 p.Thr68Ile missense_variant 0.13
fbiA 3640779 p.Trp79* stop_gained 0.13
fbiB 3641774 c.242_243delAG frameshift_variant 0.17
fbiB 3641863 p.Gly110Glu missense_variant 0.14
rpoA 3877773 c.735G>A synonymous_variant 0.14
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4038771 p.Gly645Val missense_variant 0.14
clpC1 4039003 p.Asn568Asp missense_variant 0.15
clpC1 4039018 p.Ser563Ala missense_variant 0.17
clpC1 4039022 c.1683A>G synonymous_variant 0.22
clpC1 4039031 c.1674T>C synonymous_variant 0.22
clpC1 4039363 p.Ala448Ser missense_variant 0.17
clpC1 4039592 c.1113G>T synonymous_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.14
clpC1 4039654 p.Thr351Ser missense_variant 0.17
clpC1 4039682 c.1023C>T synonymous_variant 0.2
clpC1 4039691 c.1014G>C synonymous_variant 0.31
clpC1 4039714 p.Tyr331His missense_variant 0.15
clpC1 4040057 c.648C>T synonymous_variant 0.13
embC 4240002 p.Thr47Ser missense_variant 0.14
embC 4240049 c.191dupA frameshift_variant 0.12
embC 4240692 p.Val277Ala missense_variant 0.12
embC 4240801 c.939C>T synonymous_variant 0.13
embC 4240803 p.Tyr314Phe missense_variant 0.13
embC 4241365 c.1503C>A synonymous_variant 0.15
embC 4241485 c.1623G>T synonymous_variant 0.14
embC 4242066 p.Ser735Leu missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242947 p.Gly1029Arg missense_variant 0.22
embA 4243774 p.Ala181Val missense_variant 0.18
embA 4245295 p.Thr688Met missense_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.44
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.75
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4247028 p.Leu172Arg missense_variant 0.22
embB 4247627 p.Arg372Ser missense_variant 0.17
aftB 4267472 c.1365C>T synonymous_variant 0.15
aftB 4268289 p.Val183Glu missense_variant 0.12
ethA 4326184 c.1290C>A synonymous_variant 0.13
ethA 4326822 p.Arg218Gly missense_variant 0.15
ethA 4327278 p.Phe66Ile missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408284 c.-82G>A upstream_gene_variant 0.17