Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,018,811 Δ1 bp 8.9% coding (108/810 nt) mgt ← Monofunctional glycosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,018,8110C. 8.9% 114.9 / 9.0 45coding (108/810 nt)mgtMonofunctional glycosyltransferase
Reads supporting (aligned to +/- strand):  ref base C (16/22);  new base . (2/2);  total (18/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.15e-01

CTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCCTTCTTTTAAAACTCACT  >  USA300TCH1516_ALE/2018680‑2018946
                                                                                                                                   |                                                                                                                                       
ctTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTcggc                                                                                                                                >  1:5317/1‑141 (MQ=255)
ctTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTcggcg                                                                                                                               >  2:30252/1‑141 (MQ=255)
ctTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCACGTGTAGAGAAAAAATACATGATACCAATTCATAATTCAATAAAGATACAATTAGTTATTAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTcggcg                                                                                                                               >  1:105276/1‑141 (MQ=255)
  tttATTTTCACTTTATATTATTTCATCTACATTATCGCTTGTAGATAAAAAATACATGATACCAATAAACAATGCTATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTcggcgg                                                                                                                              <  2:396074/141‑1 (MQ=255)
      ttttCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGc                                                                                                                         <  1:541933/141‑1 (MQ=255)
       tttCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTGTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGc                                                                                                                         <  1:213000/141‑1 (MQ=255)
         tCAATTTTTCTTAGTGCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTATAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCa                                                                                                                       <  1:575366/141‑1 (MQ=255)
           aaTTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAATCAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACt                                                                                                                    <  2:258390/141‑1 (MQ=255)
            aTTTTTCTTAGTTCATACACATTATTGCTTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACt                                                                                                                    <  2:93313/141‑1 (MQ=255)
              ttttCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAACCAATGCGTTAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGt                                                                                                                 >  1:289710/1‑141 (MQ=255)
                  attAGTTCATCCACATTCTAGTACGAAAAGAAAAAAGACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGTCGGTTTGCCAACTGGTTGat                                                                                                             >  2:346783/2‑141 (MQ=255)
                   ttAGTTCATCCACATTATCGCGGGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATACTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGat                                                                                                             <  1:382050/141‑1 (MQ=255)
                       ttCAACCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGataata                                                                                                         <  1:389476/141‑1 (MQ=255)
                         cATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGt                                                                                                      <  1:368699/141‑1 (MQ=255)
                            ccACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCTTTTTTCTAACTGGTTTATATTATGtttt                                                                                                   >  2:683029/1‑141 (MQ=255)
                                 ttATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGt                                                                                              <  1:678012/141‑1 (MQ=255)
                                   aTCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGa                                                                                            >  1:602718/1‑141 (MQ=255)
                                      gcgTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGt                                                                                         <  2:201694/141‑1 (MQ=255)
                                        gtgtAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGtt                                                                                        <  2:739565/141‑1 (MQ=255)
                                                  aaaaTACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCata                                                                             >  1:138474/1‑141 (MQ=255)
                                                        cATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCa                                                                       >  2:213614/1‑141 (MQ=255)
                                                              tccATTAAATAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGt                                                                 <  1:89701/140‑1 (MQ=255)
                                                                     aaCAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTT‑TTTTTCTTCGGTTTGCCAACTGGTTTATAATACGTATTATAGTGAGTTTCGTGTTTCATATGCTCATAATGTTCAtttt                                                          >  2:430013/1‑140 (MQ=255)
                                                                     aaCAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCAtttg                                                          >  1:530716/1‑141 (MQ=255)
                                                                      aCAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTTTTTTGGGGTTCGTTTTTATTATGTTTAAATTGTTCtttttt                                                         >  2:364392/1‑139 (MQ=255)
                                                                       cAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGTCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAACATGTTCAtttga                                                         >  1:255088/1‑141 (MQ=255)
                                                                          tgagATAATGATGAGGATGGTTAATAATATTTTTAGTTGTATTCGTTTAC‑TTTCTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCAtttgagttt                                                     <  2:337700/138‑1 (MQ=255)
                                                                              aTAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTT‑TTTTTCGGTGGTTTGCCAACTGGTGGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATttgagtttgagt                                                 <  1:16846/141‑1 (MQ=255)
                                                                              aTAATGATTAGAAGGGTTGATAATATTTTTAATAGGATTCGTTTAC‑TTTTTGCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATttgagtttgagt                                                 <  1:294601/141‑1 (MQ=255)
                                                                                  tGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCt                                             <  1:227842/141‑1 (MQ=255)
                                                                                   gATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCt                                             >  1:406348/1‑141 (MQ=255)
                                                                                                aataatATTCTTAATAGTATTCGTTTAC‑TTTTTTCTTTTCCGGCGGTTTGTCAACTTGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCa                               <  1:537892/141‑1 (MQ=255)
                                                                                                  taataTTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATg                             >  1:528260/1‑141 (MQ=255)
                                                                                                      atTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGtt                         <  1:213614/141‑1 (MQ=255)
                                                                                                      atTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGATTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGtt                         <  1:107869/141‑1 (MQ=255)
                                                                                                       tttttAATAGTATTCGTTTACTTTTTTTGTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTTAGTTTGAGTACCTATCGCTTCTTTTCATGCGtt                         <  2:102700/141‑1 (MQ=255)
                                                                                                              tAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTTAGTACCTATCGCTTCTTTTCATGCGTTTGCTActt                 <  1:519900/141‑1 (MQ=255)
                                                                                                                   ttCGTTTATTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTTATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTctttcttt             <  2:118413/141‑1 (MQ=255)
                                                                                                                    tttttttCTTTTTTTTTTTGAGGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCCTTCtttt            <  2:554730/138‑1 (MQ=255)
                                                                                                                    tCGTTTACTTTTTTTTTTTTTCGGTGGTTTACTAATTGGTTGATAATACGTATTATAGTTAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTTCTCCTTCtttt            <  2:514527/141‑1 (MQ=255)
                                                                                                                     cGTTTACTTTTTTT‑TTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCCTTCTTTTaa          <  2:197137/141‑1 (MQ=255)
                                                                                                                      gTTTACTTTTCTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCCTTCTTTTaa          <  1:91852/141‑1 (MQ=255)
                                                                                                                       tttACTTTTTTT‑TTTTTTGTCTGTTTGACATATGGTTGATTATATGTATTATAGTGAGGTTCGTGTTGCATTTGTTCAATATGTTCATTTGTGTTTGAGTACCTATCGTTTTTTTTCTTGCGTTCTCTCCTTCTCTTgaaa        >  2:410755/1‑141 (MQ=255)
                                                                                                                          tacttttttCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCCTTCTTTTAAAACt      >  1:325058/4‑141 (MQ=255)
                                                                                                                           acttttttCTTTTTCGGCGGTTCGCCAACTGGTTGTTAATACGTATTATAGTGAGGTTCGTGTTTCATTTGCTCAAAATGTTCATTTTAGTTTGAGTCCCTCTCGATTATATTTATCATTTTTCTCCTTCTTTTaaaatcc     >  2:689849/3‑138 (MQ=255)
                                                                                                                              tttttctttttcGGTGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCCTTCTTTTAAAACTCACt  <  2:289710/141‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                       
CTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCCTTCTTTTAAAACTCACT  >  USA300TCH1516_ALE/2018680‑2018946

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑