Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 76,969 G→A 100% intergenic (+509/‑107) USA300HOU_RS00140 → / → USA300HOU_RS00350 hypothetical protein/Monoacylglycerol lipase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE76,9690GA100.0% 93.3 / NA 27intergenic (+509/‑107)USA300HOU_RS00140/USA300HOU_RS00350hypothetical protein/Monoacylglycerol lipase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (18/9);  total (18/9)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGT  >  USA300TCH1516_ALE/76832‑77100
                                                                                                                                         |                                                                                                                                   
ctTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGt                                                                                                                                  >  1:398196/1‑141 (MQ=255)
               ttttCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTAt                                                                                                                   >  1:31979/1‑141 (MQ=255)
                 ttCGCCATGCCGCGAAATTGGCATCATGCTAGCCACTTAAGCGAACACTGCCATGATACATTAGTGGTTAGCTATATTTTTCTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTa                                                                                                                 <  1:18461/141‑1 (MQ=18)
                   cGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGCACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACt                                                                                                               <  1:402310/141‑1 (MQ=255)
                           cACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTGGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACAt                                                                                                       >  1:515432/1‑141 (MQ=255)
                                     gCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTAAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGAttttgtt                                                                                             >  1:720922/1‑137 (MQ=255)
                                      catcatGCTAGCAAGTCAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTc                                                                                            >  1:390531/1‑141 (MQ=255)
                                                     ttAAGCGAACAATGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGATCCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATGTGGGTCAAAAATTAGGGGTAt                                                                             <  1:394009/141‑1 (MQ=255)
                                                        aGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTaa                                                                          <  1:524348/141‑1 (MQ=255)
                                                             acacTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTaaaaaaa                                                                     <  1:724259/141‑1 (MQ=255)
                                                                    cATGATAAATTAGTGGTTAGCTATATTTTTTCAGTTTGGCCGTTATCCTATGAAAAACGTGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGAATTAAAAAAatgaatga                                                              >  1:366086/1‑141 (MQ=255)
                                                                          aaaTTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATa                                                        >  1:288632/1‑141 (MQ=255)
                                                                          aaaTTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATa                                                        >  1:371873/1‑141 (MQ=255)
                                                                                               tttttACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATGTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGgag                                   >  1:487708/1‑141 (MQ=255)
                                                                                                         gCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGGGAGGTTAAAAt                         >  1:26416/1‑141 (MQ=255)
                                                                                                          cAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATg                        <  1:13769/141‑1 (MQ=255)
                                                                                                             cAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGGGAGGTTAAAATGCAt                     <  1:569983/141‑1 (MQ=255)
                                                                                                             cAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCAt                     <  1:27916/141‑1 (MQ=255)
                                                                                                                aaCCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGGGGTTAAAATGCATtaa                  >  1:187980/1‑140 (MQ=255)
                                                                                                                    tataAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAGAACAATTCTCTTTGCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTAGATaa              >  1:718342/1‑141 (MQ=255)
                                                                                                                      taAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATaaaa            >  1:526293/1‑141 (MQ=255)
                                                                                                                           aaCATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTAt       <  1:428729/141‑1 (MQ=255)
                                                                                                                            aCATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATAATACTTTTATCAAGCTGATTGGCGAGGTTAAAATGCATTATATAAAATTTAtt      >  1:533794/1‑141 (MQ=255)
                                                                                                                              aTGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGa    >  1:265087/1‑141 (MQ=255)
                                                                                                                               tGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTAGTTTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAg   >  1:597198/1‑141 (MQ=255)
                                                                                                                                gggCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATGAGATTTATTGAGt  >  1:90054/1‑141 (MQ=255)
                                                                                                                                gggCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGt  >  1:23331/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                   
CTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGT  >  USA300TCH1516_ALE/76832‑77100

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑