TB-Profiler result

Run: SRR13861288
Summary

Run ID: SRR13861288

Sample name:

Date: 03-04-2023 09:28:06

Number of reads: 3363544

Percentage reads mapped: 56.11

Strain: lineage4.9

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 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 1472307 n.462C>T non_coding_transcript_exon_variant 0.15 streptomycin
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
gyrA 6700 c.-602T>C upstream_gene_variant 0.14
gyrA 6778 c.-524C>T upstream_gene_variant 0.13
gyrB 6797 p.Gly520Thr missense_variant 0.13
gyrA 7018 c.-284G>T upstream_gene_variant 1.0
gyrA 7799 c.498A>G synonymous_variant 0.16
gyrA 8204 c.903C>T synonymous_variant 0.14
gyrA 8207 c.906T>C synonymous_variant 0.14
gyrA 8442 c.1141C>T synonymous_variant 0.15
gyrA 8537 c.1236G>A synonymous_variant 0.15
gyrA 8786 c.1485T>C synonymous_variant 0.16
gyrA 8796 p.Ile499Val missense_variant 0.15
gyrA 8810 c.1509A>C synonymous_variant 0.14
gyrA 8816 c.1515C>T synonymous_variant 0.14
gyrA 8852 c.1551T>C synonymous_variant 0.14
gyrA 8858 c.1557T>C synonymous_variant 0.15
gyrA 8867 c.1566A>G synonymous_variant 0.15
gyrA 8870 c.1569G>C synonymous_variant 0.15
gyrA 8873 c.1572A>C synonymous_variant 0.15
gyrA 8897 c.1596T>C synonymous_variant 0.15
gyrA 8903 c.1602T>C synonymous_variant 0.16
gyrA 8915 c.1614A>G synonymous_variant 0.15
mshA 576668 c.1322dupA frameshift_variant&stop_gained 1.0
rpoB 760184 c.378A>G synonymous_variant 0.15
rpoB 760196 c.390C>G synonymous_variant 0.18
rpoB 760223 c.417T>C synonymous_variant 0.16
rpoB 760235 c.429T>C synonymous_variant 0.17
rpoB 760283 c.477G>C synonymous_variant 0.2
rpoB 760307 c.501T>C synonymous_variant 0.2
rpoB 760328 c.522G>C synonymous_variant 0.19
rpoB 760331 c.525G>C synonymous_variant 0.19
rpoB 760337 c.531C>G synonymous_variant 0.18
rpoB 760340 c.534G>C synonymous_variant 0.18
rpoB 760361 c.555T>C synonymous_variant 0.16
rpoB 760376 p.Asp190Glu missense_variant 0.17
rpoB 760418 c.612G>C synonymous_variant 0.15
rpoB 760925 c.1119T>C synonymous_variant 0.15
rpoB 760928 c.1122G>C synonymous_variant 0.15
rpoB 760934 c.1128C>T synonymous_variant 0.15
rpoB 760985 c.1179G>C synonymous_variant 0.14
rpoB 760991 c.1185G>C synonymous_variant 0.15
rpoB 761015 c.1209G>C synonymous_variant 0.16
rpoB 761063 c.1257C>G synonymous_variant 0.14
rpoB 761094 c.1288C>T synonymous_variant 0.14
rpoB 761171 c.1365C>T synonymous_variant 0.13
rpoB 761222 c.1416G>C synonymous_variant 0.14
rpoB 761249 c.1443A>G synonymous_variant 0.16
rpoB 761255 c.1449T>G synonymous_variant 0.16
rpoB 761261 c.1455G>T synonymous_variant 0.16
rpoB 762185 c.2379G>C synonymous_variant 0.14
rpoB 762254 c.2448T>C synonymous_variant 0.14
rpoC 763456 c.87A>G synonymous_variant 0.15
rpoC 763468 c.99G>C synonymous_variant 0.15
rpoC 763486 c.117T>C synonymous_variant 0.15
rpoC 763528 c.159G>A synonymous_variant 0.15
rpoC 763546 c.177A>G synonymous_variant 0.16
rpoC 763594 c.225C>T synonymous_variant 0.13
rpoC 763633 c.264T>C synonymous_variant 0.15
rpoC 763636 c.267T>C synonymous_variant 0.15
rpoC 763642 c.273G>C synonymous_variant 0.16
rpoC 763658 c.289_291delCTTinsTTG synonymous_variant 0.15
rpoC 763675 c.306C>G synonymous_variant 0.15
rpoC 763696 c.327T>C synonymous_variant 0.15
rpoC 763702 c.333C>G synonymous_variant 0.14
rpoC 763723 c.354G>C synonymous_variant 0.14
rpoC 763744 c.375G>C synonymous_variant 0.14
rpoC 763780 c.411C>G synonymous_variant 0.14
rpoC 763801 c.432C>G synonymous_variant 0.15
rpoC 763807 c.438T>C synonymous_variant 0.16
rpoC 763819 c.450G>C synonymous_variant 0.14
rpoC 763858 c.489A>G synonymous_variant 0.15
rpoC 763872 p.Gly168Ala missense_variant 0.15
rpoC 763876 p.Glu169Asp missense_variant 0.15
rpoC 763879 c.510A>G synonymous_variant 0.15
rpoC 763888 c.519G>C synonymous_variant 0.14
rpoC 763919 c.550C>T synonymous_variant 0.14
rpoC 763933 c.564C>T synonymous_variant 0.15
rpoC 764005 c.636G>C synonymous_variant 0.14
rpoC 764011 c.642T>C synonymous_variant 0.14
rpoC 764040 p.Ser224Asn missense_variant 0.14
rpoC 764059 c.690G>C synonymous_variant 0.14
rpoC 764720 c.1351C>T synonymous_variant 0.15
rpoC 764752 c.1383G>C synonymous_variant 0.16
rpoC 764764 c.1395T>C synonymous_variant 0.17
rpoC 764791 c.1422C>G synonymous_variant 0.18
rpoC 764809 c.1440C>T synonymous_variant 0.17
rpoC 764812 c.1443C>G synonymous_variant 0.17
rpoC 764815 c.1446A>G synonymous_variant 0.17
rpoC 764824 c.1455T>C synonymous_variant 0.17
rpoC 764830 c.1461C>G synonymous_variant 0.17
rpoC 764858 c.1489T>C synonymous_variant 0.16
rpoC 764872 c.1503A>G synonymous_variant 0.16
rpoC 764893 c.1524T>C synonymous_variant 0.14
rpoC 765100 c.1731G>C synonymous_variant 0.94
rpoC 765658 c.2289C>T synonymous_variant 0.17
rpoC 765700 c.2331T>C synonymous_variant 0.15
rpoC 765734 c.2365T>C synonymous_variant 0.14
rpoC 765739 c.2370G>C synonymous_variant 0.14
rpoC 765751 c.2382C>G synonymous_variant 0.15
rpoC 765753 p.Asp795Ala missense_variant 0.15
rpoC 765772 c.2403C>G synonymous_variant 0.14
rpoC 765784 c.2415C>G synonymous_variant 0.14
rpoC 765796 c.2427C>T synonymous_variant 0.15
rpoC 765811 c.2442T>C synonymous_variant 0.15
rpoC 765814 c.2445A>G synonymous_variant 0.15
rpoC 765835 c.2466C>T synonymous_variant 0.13
rpoC 766390 c.3021C>T synonymous_variant 0.13
rpoC 766408 c.3039C>T synonymous_variant 0.13
rpoC 766426 c.3057C>T synonymous_variant 0.15
rpoC 766738 c.3369G>T synonymous_variant 0.13
rpoC 766750 c.3381C>G synonymous_variant 0.13
rpoC 766843 c.3474T>C synonymous_variant 0.13
rpoC 766861 c.3492G>C synonymous_variant 0.15
rpoC 766864 c.3495G>C synonymous_variant 0.14
mmpL5 776059 p.Val808Met missense_variant 0.9
rpsL 781929 p.Gly124Ser missense_variant 0.12
rplC 800648 c.-161A>C upstream_gene_variant 0.16
rplC 800654 c.-155T>C upstream_gene_variant 0.15
rplC 800703 c.-106T>C upstream_gene_variant 0.14
rplC 800771 c.-38C>T upstream_gene_variant 0.14
fbiC 1303881 c.951G>C synonymous_variant 0.16
fbiC 1303884 c.954T>G synonymous_variant 0.15
fbiC 1303911 c.981G>C synonymous_variant 0.16
fbiC 1303914 c.984C>G synonymous_variant 0.17
fbiC 1303920 c.990C>G synonymous_variant 0.15
fbiC 1303923 c.993C>T synonymous_variant 0.15
fbiC 1303995 c.1065C>T synonymous_variant 0.12
fbiC 1304001 c.1071C>G synonymous_variant 0.14
fbiC 1304008 c.1078T>C synonymous_variant 0.15
fbiC 1304599 p.Ile557Phe missense_variant 0.88
fbiC 1304703 c.1773C>G synonymous_variant 0.14
fbiC 1304715 c.1785G>C synonymous_variant 0.15
embR 1417348 c.-1A>T upstream_gene_variant 1.0
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.18
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.17
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.16
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.16
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.16
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrl 1473631 n.-27T>C upstream_gene_variant 1.0
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.14
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.16
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.15
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.15
rrl 1474376 n.719T>C non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.13
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.15
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.16
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.15
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.15
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.14
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.14
rrl 1475273 n.1616T>A non_coding_transcript_exon_variant 0.14
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.14
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.14
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.15
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.15
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.15
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.14
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.16
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.16
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.18
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.19
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.16
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.16
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.15
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.15
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.13
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.15
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.15
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16
rpsA 1833667 c.126C>G synonymous_variant 0.16
rpsA 1833724 c.183C>G synonymous_variant 0.14
rpsA 1833727 c.186G>C synonymous_variant 0.15
rpsA 1833742 c.201A>G synonymous_variant 0.15
rpsA 1833745 c.204G>C synonymous_variant 0.15
rpsA 1833787 c.246C>G synonymous_variant 0.14
rpsA 1833790 c.249T>A synonymous_variant 0.15
rpsA 1833799 c.258C>G synonymous_variant 0.16
rpsA 1833811 c.270G>C synonymous_variant 0.14
rpsA 1833855 p.Lys105Thr missense_variant 0.87
rpsA 1833862 c.321G>T synonymous_variant 0.13
rpsA 1833874 c.333T>C synonymous_variant 0.14
rpsA 1834688 p.Ser383Cys missense_variant 0.13
PPE35 2170030 p.Met195Leu missense_variant 1.0
kasA 2517947 c.-168C>T upstream_gene_variant 0.14
kasA 2518276 p.Trp54* stop_gained 0.99
kasA 2518352 p.Met80Val missense_variant 1.0
kasA 2518732 c.618C>G synonymous_variant 0.14
kasA 2518783 c.669T>C synonymous_variant 0.16
kasA 2518792 c.678C>G synonymous_variant 0.16
kasA 2518795 c.681C>G synonymous_variant 0.16
eis 2714478 c.855C>A synonymous_variant 1.0
pepQ 2860170 c.248_249insA frameshift_variant 1.0
Rv2752c 3065335 p.Leu286Arg missense_variant 1.0
thyA 3073977 c.495A>G synonymous_variant 0.17
thyA 3073989 c.483T>C synonymous_variant 0.17
thyA 3074001 c.471C>G synonymous_variant 0.15
thyA 3074004 c.468T>C synonymous_variant 0.15
thyA 3074010 c.462C>G synonymous_variant 0.15
fbiB 3641019 c.-516G>A upstream_gene_variant 1.0
fbiB 3641941 p.Leu136Gln missense_variant 1.0
rpoA 3877857 c.651G>A synonymous_variant 0.15
rpoA 3877866 c.642G>C synonymous_variant 0.16
rpoA 3877872 c.636C>T synonymous_variant 0.15
rpoA 3877875 c.633T>G synonymous_variant 0.15
rpoA 3877953 c.555G>A synonymous_variant 0.14
rpoA 3877962 c.546G>T synonymous_variant 0.15
rpoA 3877989 c.519A>G synonymous_variant 0.14
rpoA 3878001 c.507A>G synonymous_variant 0.14
rpoA 3878055 c.453A>G synonymous_variant 0.14
rpoA 3878067 c.441C>G synonymous_variant 0.14
rpoA 3878070 c.438T>C synonymous_variant 0.14
rpoA 3878082 c.426T>C synonymous_variant 0.16
rpoA 3878094 c.414C>G synonymous_variant 0.15
rpoA 3878313 c.195G>C synonymous_variant 0.15
rpoA 3878334 c.174T>C synonymous_variant 0.14
rpoA 3878337 c.171T>C synonymous_variant 0.14
rpoA 3878346 c.162T>C synonymous_variant 0.14
rpoA 3878364 c.144A>G synonymous_variant 0.14
rpoA 3878370 c.138T>C synonymous_variant 0.14
rpoA 3878376 c.132G>C synonymous_variant 0.16
rpoA 3878385 c.123C>G synonymous_variant 0.14
clpC1 4038611 c.2094C>T synonymous_variant 0.14
clpC1 4039481 c.1224T>G synonymous_variant 0.14
clpC1 4039484 c.1221T>G synonymous_variant 0.14
clpC1 4039517 c.1188C>G synonymous_variant 0.14
clpC1 4039524 p.Phe394Tyr missense_variant 0.16
clpC1 4039526 c.1179G>C synonymous_variant 0.16
clpC1 4039553 c.1152C>G synonymous_variant 0.14
clpC1 4039586 c.1119G>C synonymous_variant 0.14
clpC1 4039610 c.1095G>C synonymous_variant 0.18
clpC1 4039616 c.1089G>C synonymous_variant 0.18
clpC1 4039622 c.1083C>G synonymous_variant 0.18
clpC1 4039682 c.1023C>G synonymous_variant 0.17
clpC1 4039685 c.1020C>T synonymous_variant 0.18
clpC1 4039694 c.1011G>C synonymous_variant 0.18
clpC1 4039724 c.981A>G synonymous_variant 0.19
embC 4241292 p.Leu477Gln missense_variant 1.0
embC 4242011 p.Leu717Val missense_variant 1.0
embB 4248241 c.1728C>T synonymous_variant 0.15
embB 4248265 c.1752C>T synonymous_variant 0.13
embB 4248720 p.Gly736Ala missense_variant 1.0
embB 4249469 p.Leu986Met missense_variant 0.13
embB 4249676 p.Arg1055Cys missense_variant 1.0
aftB 4267927 p.Ala304Ser missense_variant 0.98