Find_novel_viruses_C_novel_cov - ababaian/serratus GitHub Wiki

Microassembly Coronaviridae Fragments

Pungitius pungitius (Ninespine Stickleback) SRR2976063

DIAMOND search results

SRR2976063_NODE_10_length_227_cov_1.883117
ERR3994223.Epsy.StypNV 76%

Microassembly:

>SRR2976063_NODE_10_length_227_cov_1.883117
CGCCTATTTCTTTACTCCAGTATGTACGAACATGGTGATTTGGACTCTGCTTCCACGCTA
TTGTTCGAGCATATGCAACACACATGCCCTCTGATGATTCTTTCAGATGACGGCGTTGCT
GGACCTTTAACTGACGACCCAACTGCATGCTGTCTTGATGATTTTAAAGCTACGCTGTAC
TACCAGAACAACGTATATCTTTCTGATGAAAAGTGCTGACCTTGCTA

>SRR2976063_NODE_10_length_227_cov_1.883117_translated
EHMQHTCPLMILSDDGVAGPLTDDPTACCLDDFKATLYYQNNVYLSDEKC

SRA
BLAST 58.57% to PSNV (will expire)

SchauNV - Siniperca chuatsi (Chinese Perch) SRR13002565

DIAMOND:

SRR13002565_NODE_2_length_242_cov_0.911243
QEG08237.1.PsNV	72.7	1.55E-34

Microassembly:

>SRR13002565_NODE_2_length_242_cov_0.911243
GGTCCATGTATGTAAATATTACGATACAGATTATGTACGAAAGAACGGTTGGCAGCGGCT
GTGTTTTGAATAGCCTTGTTAACAGAAGTGGTAACAACCTGAAAGAGGTTGAAAGCACTG
TTAGCATAGGCCGTAGTTGAATCACCACTACTAGTACCACCGGGTTTCCTAAAGAAACTA
CCGTTAACGACACAAGTTTCTGAAAGAACTTGAGACATTTCGTTAGCGAGTCTGTACTTC
TT

>SRR13002565_NODE_2_length_242_cov_0.911243_translated
MSQVLSETCVVNGSFFRKPGGTSSGDSTTAYANSAFNLFQVVTTSVNKAIQNTAAANRSF
VHNLYRNIYIHG

SRA
BLAST 72% to PsNV

PmexiNV: Poecilia mexicana (Shortfin Molly) SRR5224039

DIAMOND:

SRR5224039_NODE_1_length_291_cov_1.289256
QEG08237.1.PsNV 74.4	4.35E-41

Microassembly:

>SRR5224039_NODE_1_length_291_cov_1.289256
GTTCATTGGTAGTGTTGTTTTGAAGAGGCCAGTCGCGACGGACTATAGAGTCAATAGCAC
TGGTTATAACCTGAAATAAGTTAAAAGCGGAATTGGCGTAAGCGGTAGTGCCGTCACCTG
AGGAAGTACCCCCAGGTTTACGGTAAAGGTAACCGTTCACTAGACAAGTCTCGCTAAGAA
CCTGTTGCATTTCATTTGCAAGGCGATACAACTTATCAGGGTGCTGACAACAGTCAATGT
GCTTATTCAGAAATAGCCAAGCAGCAGACTGACGTAAGAGGTTAGGCATGG

>SRR5224039_NODE_1_length_291_cov_1.289256_translated
MPNLLRQSAAWLFLNKHIDCCQHPDKLYRLANEMQQVLSETCLVNGYLYRKPGGTSSGDG
TTAYANSAFNLFQVITSAIDSIVRRDWPLQNNTTNE

SRA BLAST 75% to PsNV: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=DY3HADZW013 (edited)

PdisjNV - Pterygoplichthys disjunctivus (Vermiculated sailfin catfish) SRR2290960

DIAMOND:

SRR2290960_NODE_1_length_273_cov_1.803571
77.8%

Microassembly:

>SRR2290960_NODE_1_length_273_cov_1.803571
TAAGTACTCTATATCCAGTAAAGCTAGGGCTCGTACTGTGGCAGGTGTTTCTATTCTTTC
AACTGCCCTTAATCGTATGACTCATCAGCATTTACTTAAAGATATAGCAGCTGCCAGGGA
TAAAACTGTTTGCATTGGCACTCCTAAGTTTTATGGTAATTGGCACCTAATGATGTCACG
CTTTTTGGACGACAAACCTCGTCGTTTGATAGGTTGGGACTACCCTAAGTGTGACCGTTC
CATGCCTAACCTTATTCGCATGGCATCGTGTAT

>SRR2290960_NODE_1_length_273_cov_1.803571_translated
KYSISSKARARTVAGVSILSTALNRMTHQHLLKDIAAARDKTVCIGTPKFYGNWHLMMSR
FLDDKPRRLIGWDYPKCDRSMPNLIRMASC

SRA
BLAST 72% to PsNV

envNV 1 - Freshwater Environmental SRR6281441

DIAMOND:

SRR6281441_NODE_69_length_424_cov_0.950166
QEG08237.1.PsNV 58.8

Microassembly:

>SRR6281441_NODE_69_length_424_cov_0.950166
AGCTCACACTGCGTCTTCAGTACCAACTATTGATACTCGTACAGACATTTATTGTGCTGG
TTCCAATCGTATTGTTCCAGGAAAGATACTTAAGCCTGCTAATATTGACTTTGCTTTTGT
AGAATTTGCTAAAAAGACTCTACTCTTTGAAGGCTCTCCTATAAAACTAAGTCATTTCTT
CTTTCTTGCCAATCGTGACTCTACTATTAAGGATTTTGACTATTATCGTTATAATATACC
CACAGTACTTGATATTAAACAGTTCCTCTTTACATACCAGGTTGTTTGTAAATATTTTGA
TGTTTACAATGCTGGATGTATATGTAGTTCTTCTGTTGTAGTTAATAACCCCAAGAAGTC
TGCCGGCTTTCCATTCAATATGTTTGGTTGTGCCGATGAAGTTCTTGACTATTTAGGACA
TGAC

>SRR6281441_NODE_69_length_424_cov_0.950166_translated
AHTASSVPTIDTRTDIYCAGSNRIVPGKILKPANIDFAFVEFAKKTLLFEGSPIKLSHFF
FLANRDSTIKDFDYYRYNIPTVLDIKQFLFTYQVVCKYFDVYNAGCICSSSVVVNNPKKS
AGFPFNMFGCADEVLDYLGHD

SRA
BLAST: 57% to PsNV

envNV 2 - Seawater Metatranscriptome ERR3588795

DIAMOND:

ERR3588795_NODE_755_length_225_cov_1.013158
SRR10917299.TparNV 74.3%

Microassembly:

>ERR3588795_NODE_755_length_225_cov_1.013158
CGGCATAGAACGATCACATTTAGGGTAATCCCAACCAAACAAGGTACGGCTGTGCCCGTC
ATTAAAACGAAGAAGCATCCTGTGCCAGTGTCCATAGAATTTAGGAGTACCTATAACACA
TGTTTGGTCTCTACCTGCAGCTATATTTTTCAACAGTTTCTGATGACAGCAACGGTTTAA
AATAGTAGACAAAATGCTTACACCAGCAATGGTGCGAGCTCTGGG

>ERR3588795_NODE_755_length_225_cov_1.013158_translated
PRARTIAGVSILSTILNRCCHQKLLKNIAAGRDQTCVIGTPKFYGHWHRMLLRFNDGHSR
TLFGWDYPKCDRSMP

SRA
BLAST 74% to PsNV

LpipiLV - Lithobates pipiens (Northern leopard frog) SRR1185235

DIAMOND:

SRR1185235_NODE_1_length_372_cov_2.241486
SRR2418623.MeLV 63.9%

Microassembly:

>SRR1185235_NODE_1_length_372_cov_2.241486
GGTAGTTATAAATTGAATGATGTTAAAAACAGAATTAGCGGGTGCTGTAGTTGCATCACC
GCTAGAAGTACCACCAGGTTTGGTATAAAAAGAACCATTAACAAAAACGTATTCGTTAAT
AACCTGAGCGTGTTCGTTGACTAATCTATAAAATTTATCAGAATTAGAACAACAATCTTT
GTGTGATCGTAATAATGTTAAACATGAAGCTACACGAATAATATTAGGCATAGCACGATC
ACATTTAGGATAATCCCATCCATAGAGAACAGGGTTGTTTATATTGGTAATCATACGTTT
GAGCATAGAATCCCAACCACCGTAATATTTAGTTCTACCTATAACAATGGTAGCATCAGG
TGTAGAAGTAAT

>SRR1185235_NODE_1_length_372_cov_2.241486_translated
ITSTPDATIVIGRTKYYGGWDSMLKRMITNINNPVLYGWDYPKCDRAMPNIIRVASCLTL
LRSHKDCCSNSDKFYRLVNEHAQVINEYVFVNGSFYTKPGGTSSGDATTAPANSVFNIIQ
FITT

SRA
BLAST 63.7% to Pecari tajacu coronavirus

Off-targets

Mneid-associated Mesonivirus - Malus neidzwetzkyana (Rose sp.) SRR7719395

DIAMOND:

SRR7719395_NODE_115_length_207_cov_1.639241
QEG08237.1.PsNV 41.5%

Microassembly:

>SRR7719395_NODE_115_length_207_cov_1.639241
CCAACATCTACTATTAAAGTTCGTAACCCCCATAAATCTTCAGGCATACCTTACCGTAAT
TACGGTGATGCTGAATTTATGCGTGATTTATATGGTAAAGACCGTGATAAAATAACTTTA
CACAAAACTCATTCCGCTGATCCATCTTTTACGCTTGTTATAAATAAAGTAGCTATATCT
ACAAAACCACGTGACCGTACTATTTTA

>SRR7719395_NODE_115_length_207_cov_1.639241_translated
PTSTIKVRNPHKSSGIPYRNYGDAEFMRDLYGKDRDKITLHKTHSADPSFTLVINKVAIS
TKPRDRTIL

SRA
BLAST 98% to AC Meson-like:

Aphis citricidus meson-like virus

Query  1    PTSTIKVRNPHKSSGIPYRNYGDAEFMRDLYGKDRDKITLHKTHSADPSFTLVINKVAIS  180
            PTSTIKVRNPHKSSGIPYRNYGDAEFMRDLYGK+RDKITLHKTHSADPSFTLVINKVAIS
Sbjct  509  PTSTIKVRNPHKSSGIPYRNYGDAEFMRDLYGKERDKITLHKTHSADPSFTLVINKVAIS  568

Query  181  TKPRDRTIL  207
            TKPRDRTIL
Sbjct  569  TKPRDRTIL  577

Ochin Mesonivirus - Oxya chinensis (Rice Grasshopper) SRR8946811

DIAMOND:

SRR8946811_NODE_17_length_330_cov_0.894942
QEG08237.1.PsNV	39.7%

Microassembly:

>SRR8946811_NODE_17_length_330_cov_0.894942
CTGCGTCCAGCTTCGCTTTTGTTGGAATTAATAGCAAGGATTGTGCGGTCGCGATGCTTT
GTACTGAGGGCAACTTTATTGATTACAAGGGTGAGATTTTGATCAGAAGAGTGTTGTTTG
TGTGCAACAATTTTGTCTCGGTGTTCTCCATATATGTCTCGTATAAATTGGCCATCTCCG
TGATTTCTATAGGGAATGCCTGAGGATTTATGTTTATTGCGAATTTTGACAGAGGAGACG
GGGGTGACACAATTAGGTTTACCATCTGAAGTGCATACTTCGCTGCGCAATAAAAATGTA
ACAGCTTCAACAATAAAAAGTAGGTTGACA

>SRR8946811_NODE_17_length_330_cov_0.894942_translated
VNLLFIVEAVTFLLRSEVCTSDGKPNCVTPVSSVKIRNKHKSSGIPYRNHGDGQFIRDIY
GEHRDKIVAHKQHSSDQNLTLVINKVALSTKHRDRTILAINSNKSEAGR

SRA
BLAST 66.97% to AC Meson-like:

Aphis citricidus meson-like virus - 

Query  329  VNLLFIVEAVTFLLRSEVCTSDGKPNCVTPVSSVKIRNKHKSSGIPYRNHGDGQFIRDIY  150
            VNLL   E V   LRS V  +DGKP+ V P S++K+RN HKSSGIPYRN+GD +F+RD+Y
Sbjct  480  VNLLMCYEYVLHKLRSRVVATDGKPSIVLPTSTIKVRNPHKSSGIPYRNYGDAEFMRDLY  539

Query  149  GEHRDKIVAHKQHSSDQNLTLVINKVALSTKHRDRTILAINSNKSEAGR  3
            G+ RDKI  HK HS+D + TLVINKVA+STK RDRTILAINSNKSE GR
Sbjct  540  GKERDKITLHKTHSADPSFTLVINKVAISTKPRDRTILAINSNKSECGR  588