TB-Profiler result

Run: ERR4820192
Summary

Run ID: ERR4820192

Sample name:

Date: 01-04-2023 16:32:17

Number of reads: 323869

Percentage reads mapped: 83.12

Strain: La3

Drug-resistance: Other

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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
La3 M.orygis None 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.85 streptomycin
pncA 2288847 p.Gly132Asp missense_variant 0.22 pyrazinamide
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 5516 p.Ile93Val missense_variant 1.0
gyrB 6109 c.870G>A synonymous_variant 1.0
gyrB 6227 p.Lys330Glu missense_variant 0.15
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrB 6621 p.Asp461Gly missense_variant 0.18
gyrB 6717 p.Ile493Thr missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7858 p.Ala186Val missense_variant 0.29
gyrA 8930 c.1629C>T synonymous_variant 1.0
gyrA 9110 c.1809G>A synonymous_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9712 p.Met804Lys missense_variant 0.13
fgd1 490661 c.-122_-121insGCGAGC upstream_gene_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.3
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491749 p.Leu323Phe missense_variant 1.0
ccsA 620361 c.471C>T synonymous_variant 0.15
ccsA 620839 c.949C>T synonymous_variant 0.2
rpoB 760408 p.Ser201Asn missense_variant 0.17
rpoB 761049 p.Arg415Trp missense_variant 0.2
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoB 761557 p.Ala584Gly missense_variant 0.29
rpoB 761562 p.Ala586Ser missense_variant 0.29
rpoB 761565 p.Met587Leu missense_variant 0.29
rpoB 761570 c.1764T>C synonymous_variant 0.29
rpoB 761600 c.1794T>C synonymous_variant 0.29
rpoB 761612 c.1806G>C synonymous_variant 0.33
rpoB 761615 c.1809A>C synonymous_variant 0.33
rpoB 761633 c.1827G>C synonymous_variant 0.33
rpoB 761642 c.1836G>C synonymous_variant 0.22
rpoB 761643 p.Val613Ile missense_variant 0.22
rpoB 761649 p.Ser615Pro missense_variant 0.29
rpoB 761654 p.Glu616Asp missense_variant 0.29
rpoB 762352 c.2557_2562dupGACGAG conservative_inframe_insertion 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763056 p.Thr1084Ala missense_variant 0.22
rpoC 763483 c.114G>C synonymous_variant 0.25
rpoC 763486 c.117T>C synonymous_variant 0.25
rpoC 763492 c.123G>C synonymous_variant 0.25
rpoC 763504 c.135C>T synonymous_variant 0.25
rpoC 763528 c.159G>C synonymous_variant 0.25
rpoC 763531 c.162G>C synonymous_variant 0.22
rpoC 763534 c.165T>C synonymous_variant 0.22
rpoC 763537 c.168C>G synonymous_variant 0.2
rpoC 763546 c.177A>G synonymous_variant 0.14
rpoC 763550 p.Tyr61Ala missense_variant 0.14
rpoC 763570 c.201G>C synonymous_variant 0.13
rpoC 763578 p.Phe70Tyr missense_variant 0.13
rpoC 763585 c.216C>G synonymous_variant 0.13
rpoC 763589 p.Ile74Val missense_variant 0.12
rpoC 763600 c.231C>T synonymous_variant 0.12
rpoC 763606 c.237C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775967 p.Met838Ile missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776541 p.Ser647Asn missense_variant 0.17
mmpL5 777613 p.Gly290Arg missense_variant 0.25
mmpL5 778086 c.394dupG frameshift_variant 1.0
mmpR5 779011 p.Asp8Asn missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
embR 1416964 c.384C>G synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471755 n.-91C>A upstream_gene_variant 0.14
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.88
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.88
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.4
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.45
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.45
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.91
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.83
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.83
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.45
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.91
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.9
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.9
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.54
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.92
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.9
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.89
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.89
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.22
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.6
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.6
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.8
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.18
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.92
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.27
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.89
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.89
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.84
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.84
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.58
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.6
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.55
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.5
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.33
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.29
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.5
rrs 1472970 n.1125C>T non_coding_transcript_exon_variant 0.29
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.5
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.57
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.22
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.44
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.25
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.57
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.5
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.62
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.43
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.5
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.29
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.43
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.43
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.43
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.38
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.43
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.29
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.29
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.33
rrl 1474686 n.1029A>G non_coding_transcript_exon_variant 0.5
rrl 1474695 n.1038A>G non_coding_transcript_exon_variant 0.4
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.67
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.67
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.67
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.67
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.67
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.6
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.5
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.5
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.33
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.33
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.29
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.29
rrl 1476664 n.3007T>G non_coding_transcript_exon_variant 1.0
inhA 1673680 c.-522C>G upstream_gene_variant 1.0
rpsA 1834363 c.822G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918541 p.Pro201Gln missense_variant 0.2
katG 2154707 p.Val469Leu missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156094 c.18A>G synonymous_variant 0.12
PPE35 2167697 c.2916C>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168922 p.Thr564Arg missense_variant 1.0
PPE35 2169279 c.1312_1333delAACAATGGTGTCTTTTACCGTG frameshift_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.29
PPE35 2169910 p.Asn235Tyr missense_variant 0.38
PPE35 2169924 p.Ala230Leu missense_variant 0.18
PPE35 2170147 p.Ser156Ala missense_variant 0.17
PPE35 2170457 c.156G>C synonymous_variant 0.29
PPE35 2170460 c.153G>A synonymous_variant 0.25
PPE35 2170465 p.Ala50Ser missense_variant 0.2
PPE35 2170472 c.141G>A synonymous_variant 0.25
PPE35 2170669 c.-57G>A upstream_gene_variant 1.0
Rv1979c 2221771 p.Leu465Pro missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222919 c.246A>G synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289978 c.-737T>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726166 c.-27T>A upstream_gene_variant 0.17
ahpC 2726378 c.186T>A synonymous_variant 0.83
folC 2746391 p.Val403Ala missense_variant 1.0
pepQ 2860027 p.Leu131Pro missense_variant 0.22
ribD 2986800 c.-39T>C upstream_gene_variant 0.18
Rv2752c 3065414 p.Ser260Thr missense_variant 0.29
Rv2752c 3067009 c.-818A>G upstream_gene_variant 1.0
thyX 3067812 p.Gln45Arg missense_variant 1.0
thyA 3073969 p.Ala168Val missense_variant 0.22
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475113 c.1107G>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475323 c.1317T>C synonymous_variant 1.0
Rv3236c 3612694 c.423T>C synonymous_variant 1.0
fbiB 3641584 p.Val17Ala missense_variant 1.0
fbiB 3642608 c.1074C>T synonymous_variant 0.15
clpC1 4038428 c.2277G>A synonymous_variant 0.29
clpC1 4039645 p.His354Asp missense_variant 0.22
clpC1 4039853 c.852G>A synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241463 p.Arg534His missense_variant 0.14
embC 4242033 p.Thr724Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244154 p.Thr308Ala missense_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246848 p.Gln112Arg missense_variant 0.18
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247068 c.555T>C synonymous_variant 0.5
embB 4247470 c.957T>C synonymous_variant 0.33
embB 4247472 p.Phe320Tyr missense_variant 0.33
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267045 p.Thr598Ser missense_variant 0.18
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326431 p.Leu348Pro missense_variant 0.17
ethA 4326456 p.Thr340Ala missense_variant 0.15
ethA 4327042 p.Asp144Asn missense_variant 1.0
ethA 4328211 c.-738A>G upstream_gene_variant 1.0
ethA 4328283 c.-810G>A upstream_gene_variant 0.12
whiB6 4338269 p.Gly85Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408253 c.-51A>G upstream_gene_variant 0.2