Predicted mutation
evidence seq id position mutation annotation gene description
RA CP009273 468,126 Δ1 bp coding (73/339 nt) glnK → nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP009273468,1260A.97.1% 146.7 / ‑2.6 34coding (73/339 nt)glnKnitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base . (15/18);  total (16/18)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

TTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGC  >  CP009273/467983‑468250
                                                                                                                                               |                                                                                                                             
ttCTGGCACCACGCTTGCAATACCTGCTGCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTCGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAgg                                                                                                                         <  1:490867/149‑1 (MQ=255)
   tGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGcc                                                                                                                      >  1:118252/1‑149 (MQ=255)
        cacCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑cc                                                                                                                <  2:135791/149‑1 (MQ=255)
                   aTACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGt                                                                                                     >  1:396920/1‑149 (MQ=255)
                               tgtAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCgg                                                                                         <  2:702437/149‑1 (MQ=255)
                               tgtAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCgg                                                                                         <  2:625198/149‑1 (MQ=255)
                                          gcttACCGAATTCTGGCCGGAGGGGATCTATGAAGCTGGTGACGGTTATTATCAAACCATTCAGGCTGGAAGACAATCGAGAATCTAGATCTTCCGTTGGT‑TTCAGGGCCTGA‑CCGTCACCTAAGTGAAAGGTTGCGGGCGTAAGAAAg                                                                              <  1:322219/147‑1 (MQ=255)
                                              aCCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGCAGACGTTCGTGAAGCGTTATCTTACATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAAGTTTCTGGCGTCAGAAAGGGCa                                                                          >  1:601582/1‑149 (MQ=255)
                                                cGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATg                                                                        >  1:354022/1‑149 (MQ=255)
                                                cGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTAGCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATg                                                                        <  2:701235/149‑1 (MQ=255)
                                                         aCCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGt                                                               >  2:409339/1‑149 (MQ=255)
                                                                 ggATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCggggg                                                       <  1:312410/149‑1 (MQ=255)
                                                                       ttGAAGCTGGTGATCGTGATGATCAAACCATTCTAGCTGGAAGTCGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGG‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGaa                                                 <  2:381276/148‑1 (MQ=255)
                                                                             cTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTGCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGc                                           <  2:118252/149‑1 (MQ=255)
                                                                              tgttGACCGGGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGGCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCg                                          <  2:303805/146‑1 (MQ=255)
                                                                                  taCCGTGATAATCAAACCATTCAAGCGGGAAGAGGTTCGTGAAGCGTTATCTTCCATTTGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCaa                                      <  2:164745/148‑1 (MQ=255)
                                                                                       tGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTcc                                 <  2:117330/149‑1 (MQ=255)
                                                                                       tGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTACCTTCCATTGGT‑TTCCGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTcc                                 >  1:572058/1‑149 (MQ=255)
                                                                                          tAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGc                              <  2:396920/149‑1 (MQ=255)
                                                                                           aaTCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAGAGGGCATGCCGGGCTGTACCGGGGGGCGGAAGACAGCGTCAATTTCCTGcc                             >  2:142473/1‑149 (MQ=255)
                                                                                           aaTCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGcc                             >  1:296513/1‑149 (MQ=255)
                                                                                             tCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCATTTTCGTGCCaa                           >  1:437012/1‑149 (MQ=255)
                                                                                             tCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCaa                           >  2:60761/1‑149 (MQ=255)
                                                                                               aaaCCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCaaaa                         >  1:74496/1‑149 (MQ=255)
                                                                                               aaaCCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCaaaa                         >  2:39130/1‑149 (MQ=255)
                                                                                                 aCCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTA‑TCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGACGTCAGAAAGGGCATGCCGAGCTGTACTGGGGGGCGGAATACAGCGTCAATTTCCTGCCGAAGGt                       >  1:579384/1‑149 (MQ=255)
                                                                                                     ttCAAGGTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTaaaa                   <  2:494448/149‑1 (MQ=255)
                                                                                                     ttCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCATCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCCAAGGTaaaa                   >  1:499624/1‑149 (MQ=255)
                                                                                                        aaGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAAtt                >  2:511012/1‑149 (MQ=255)
                                                                                                          gCTGGAAGACGTTCGGGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGAGCCCTCTCTG‑AGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGa              <  2:601582/149‑1 (MQ=255)
                                                                                                           cTGGAAGACGTTCGTGGAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGAt             <  2:42449/149‑1 (MQ=255)
                                                                                                               aaGACGTTCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCAGAGCTGCATCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTgg         <  2:151861/149‑1 (MQ=255)
                                                                                                                     ttCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGAtta   >  1:47800/1‑148 (MQ=255)
                                                                                                                      tCGTGAAGCGTTATCTTCCATTGGT‑TTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGc  <  2:354022/149‑1 (MQ=255)
                                                                                                                                               |                                                                                                                             
TTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGA‑CCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGC  >  CP009273/467983‑468250

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: ‑