TB-Profiler result

Run: SRR1140723
Summary

Run ID: SRR1140723

Sample name:

Date: 02-04-2023 20:57:59

Number of reads: 470100

Percentage reads mapped: 18.28

Strain: lineage4.6.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.99
lineage4.6.1.1 Euro-American T2-Uganda RD724 0.99
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 5315 p.Val26Ile missense_variant 0.22
gyrA 7352 c.51G>T synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8857 p.Thr519Ile missense_variant 0.14
gyrA 8865 p.Glu522* stop_gained 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575426 p.Ser27Pro missense_variant 0.25
ccsA 620354 p.Trp155Leu missense_variant 0.22
ccsA 620675 c.789delC frameshift_variant 0.2
rpoB 762837 p.Glu1011Lys missense_variant 0.33
rpoC 762887 c.-483G>C upstream_gene_variant 0.56
rpoC 762899 c.-471G>C upstream_gene_variant 0.67
rpoC 762917 c.-453C>G upstream_gene_variant 0.6
rpoC 762920 c.-450C>T upstream_gene_variant 0.6
rpoC 762923 c.-447C>G upstream_gene_variant 0.6
rpoB 762925 p.Thr1040Ile missense_variant 0.6
rpoB 762934 c.3129_3130insAGCC frameshift_variant 0.56
rpoB 762938 c.3133_3136delATGA frameshift_variant 0.56
rpoC 762989 c.-381G>C upstream_gene_variant 0.38
rpoC 762995 c.-375G>T upstream_gene_variant 0.36
rpoC 764198 p.Leu277Val missense_variant 0.2
rpoC 764512 c.1143G>A synonymous_variant 0.15
rpoC 764557 p.Asn396Lys missense_variant 0.17
rpoC 764566 c.1197C>G synonymous_variant 0.36
rpoC 764575 c.1206T>G synonymous_variant 0.47
rpoC 764581 c.1212T>C synonymous_variant 0.5
rpoC 764582 p.Leu405Met missense_variant 0.47
rpoC 764587 c.1218C>G synonymous_variant 0.56
rpoC 764593 c.1224C>T synonymous_variant 0.55
rpoC 764605 c.1236G>C synonymous_variant 0.57
rpoC 764611 c.1242G>T synonymous_variant 0.59
rpoC 764632 c.1263T>C synonymous_variant 0.67
rpoC 764641 c.1272C>T synonymous_variant 0.65
rpoC 764650 c.1281G>T synonymous_variant 0.71
rpoC 764663 p.Val432Thr missense_variant 0.5
rpoC 764672 p.Gln435Glu missense_variant 0.64
rpoC 764677 c.1308C>G synonymous_variant 0.42
rpoC 764695 c.1326T>C synonymous_variant 0.3
rpoC 766889 p.Glu1174* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775936 p.Asp849Tyr missense_variant 0.22
mmpR5 778127 c.-863G>C upstream_gene_variant 0.15
mmpR5 778457 c.-533C>T upstream_gene_variant 0.17
mmpL5 778663 c.-183C>A upstream_gene_variant 0.29
mmpL5 779118 c.-638C>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303875 c.945G>C synonymous_variant 0.5
fbiC 1304117 p.Pro396His missense_variant 0.12
fbiC 1304812 p.Met628Leu missense_variant 0.13
fbiC 1304920 p.Ile664Phe missense_variant 0.25
embR 1417256 p.Gly31Asp missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 0.45
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.45
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.45
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.59
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.8
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.76
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.71
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.69
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.69
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.59
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.55
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.53
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.44
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.47
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.38
rrs 1472298 n.453G>C non_coding_transcript_exon_variant 0.25
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.45
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.5
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.67
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.69
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.67
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.67
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.67
rrs 1472386 n.541G>A non_coding_transcript_exon_variant 0.12
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.56
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.35
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.35
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.29
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.54
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.59
rrs 1472694 n.849C>G non_coding_transcript_exon_variant 0.22
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.42
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.69
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.72
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.73
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.92
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.86
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.82
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.82
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.79
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.83
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.79
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.79
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.38
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.25
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.29
rrs 1473223 n.1378G>A non_coding_transcript_exon_variant 0.29
rrs 1473352 n.1507C>G non_coding_transcript_exon_variant 0.43
rrs 1473353 n.1508C>G non_coding_transcript_exon_variant 0.43
rrs 1473358 n.1513G>C non_coding_transcript_exon_variant 0.43
rrs 1473359 n.1514G>C non_coding_transcript_exon_variant 0.43
rrl 1473461 n.-197T>A upstream_gene_variant 0.29
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.3
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.3
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 0.33
rrl 1474876 n.1219T>A non_coding_transcript_exon_variant 0.33
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.3
rrl 1475499 n.1842C>G non_coding_transcript_exon_variant 0.17
rrl 1475526 n.1869C>T non_coding_transcript_exon_variant 0.17
rrl 1475707 n.2050T>C non_coding_transcript_exon_variant 0.67
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.67
rrl 1475716 n.2059A>C non_coding_transcript_exon_variant 0.5
rrl 1475735 n.2078T>C non_coding_transcript_exon_variant 0.33
rrl 1475736 n.2079G>T non_coding_transcript_exon_variant 0.33
rrl 1475790 n.2133C>A non_coding_transcript_exon_variant 0.17
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.2
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.67
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.67
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.71
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.73
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.72
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.71
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.5
rrl 1476232 n.2575G>C non_coding_transcript_exon_variant 0.25
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.18
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.18
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.27
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.73
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.79
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.79
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.8
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.84
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.84
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.86
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.87
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.88
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.89
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.83
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.83
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.78
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.78
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.75
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.58
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.36
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.32
rrl 1476739 n.3082T>A non_coding_transcript_exon_variant 0.18
rpsA 1834723 p.Glu394Asp missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101865 p.Trp393Ser missense_variant 0.14
katG 2154140 p.Phe658Leu missense_variant 0.25
katG 2154187 p.Pro642Gln missense_variant 0.2
PPE35 2168636 c.1977G>A synonymous_variant 0.18
PPE35 2168762 c.1850delC frameshift_variant 0.18
PPE35 2170791 c.-179A>G upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714422 p.Ala304Glu missense_variant 0.33
eis 2714460 c.873G>A synonymous_variant 0.33
Rv2752c 3065364 c.828G>C synonymous_variant 0.29
thyX 3067472 c.474C>G synonymous_variant 0.18
thyX 3067634 c.312C>T synonymous_variant 0.25
fbiD 3339267 c.150G>A synonymous_variant 0.18
Rv3083 3448532 p.Ile10Thr missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474314 p.Ala103Val missense_variant 0.25
fprA 3474477 p.Asn157Lys missense_variant 0.29
fprA 3474489 p.Asp161Glu missense_variant 0.2
whiB7 3568523 c.157T>C synonymous_variant 0.33
whiB7 3568735 c.-56G>A upstream_gene_variant 0.2
whiB7 3568806 c.-127G>T upstream_gene_variant 0.15
fbiB 3642411 c.877C>A synonymous_variant 0.18
clpC1 4039496 p.Ile403Met missense_variant 0.18
clpC1 4039520 c.1185G>C synonymous_variant 0.22
clpC1 4039526 c.1179G>C synonymous_variant 0.22
clpC1 4039533 p.Asn391Thr missense_variant 0.2
clpC1 4039546 p.Asp387Asn missense_variant 0.2
clpC1 4039739 c.966C>G synonymous_variant 0.29
clpC1 4040269 p.Gln146Lys missense_variant 0.13
clpC1 4040308 c.397C>A synonymous_variant 0.18
clpC1 4040503 p.Gly68Cys missense_variant 0.18
embC 4240702 c.840G>T synonymous_variant 0.33
embC 4241985 p.Leu708Ser missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245352 p.Lys707Arg missense_variant 0.15
aftB 4267095 p.Pro581Gln missense_variant 0.22
ethA 4327995 c.-522C>T upstream_gene_variant 0.15
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0