Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 468,144 Δ1 bp 27.8% coding (91/339 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
*CP009273468,1440A.27.8% 35.7 / 13.1 18coding (91/339 nt)glnKnitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB
Reads supporting (aligned to +/- strand):  ref base A (4/9);  new base . (3/2);  total (7/11)
Fisher's exact test for biased strand distribution p-value = 3.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTC  >  CP009273/468007‑468284
                                                                                                                                         |                                                                                                                                             
ttctgcGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGCAGATATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAg                                                                                                                                   <  1:309456/149‑1 (MQ=255)
        ggaGCAGAACCTTTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCgg                                                                                                                            <  1:232407/147‑1 (MQ=255)
                      aCCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGa                                                                                                                    <  2:72423/143‑1 (MQ=255)
                       ccGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCAt                                                                                                            >  1:365/1‑149 (MQ=255)
                                             cTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCg                                                                                      <  1:309970/149‑1 (MQ=255)
                                             cTAGGAAGCTGGTGACCGTGATAACCAAACCATTCATGCGTTAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCg                                                                                      <  1:7901/149‑1 (MQ=255)
                                                                  tAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGTGTTATATTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCTTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCGGAATACATCGTCAATTTCCTg                                                                 <  1:233814/149‑1 (MQ=255)
                                                                         aCCATTCAAGCTGGAAGACCGTCGGGGAGCGTTATCTTCCATTGGGATTCAGGGCCTGACCCGC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATTCCGAGCTGTACCGGGGGGGCGGAATACAGCGTCAATTTCCTGc                                                                <  2:251483/143‑1 (MQ=255)
                                                                            aTTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCGGAATACAGCGTCAGTTTCCTGCCaa                                                             >  2:139100/1‑143 (MQ=255)
                                                                             ttCAAGCTGGAAGACGTTCGTGAAGCGGTATCCTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGCGCGGAATACAGCGTCAATTTCCTGCCAAAAGTaaa                                                      <  1:12868/149‑1 (MQ=255)
                                                                                  gCTGGAAGACGTTCGTGACGCGTTATCTTCCATTGGTATTCAGGGCCTGCCCGTCACCGAAGAGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCGGAATACAGCGTCCATTTCCTGCGCAAAGTac                                                       >  2:86405/1‑142 (MQ=255)
                                                                                      gAAGACGTTCGTGAAGCGTTATCTTACATTTGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGAtgtg                                            >  1:171537/1‑149 (MQ=255)
                                                                                         gACGTGCGTGAAGCGTTATCTTCCATTGGTAAACAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCGGTGCC‑GGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTaaaaccgga                                                >  2:177156/1‑138 (MQ=255)
                                                                                          aCGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGTCGAGCTGTACC‑GGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGAt                                               <  2:86472/143‑1 (MQ=255)
                                                                                                      cGTTATCTTCCATTGGTATGCAGGGCCGGACCGTCAACGAAGGGAATGGTGTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑‑GGGGGCGGAATACAGCGGCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCtg                                  <  2:193046/143‑1 (MQ=255)
                                                                                                        ttATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCGGAATAAAGCGTCATTTACCTGCCAAAAGTAAAAATTGATGTGGCGATTCATGATGACCaa                          >  1:127133/1‑149 (MQ=255)
                                                                                                                 aTTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGGTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATgt                  >  1:198785/1‑148 (MQ=255)
                                                                                                                                       ccACCGAAGTGAAGGGTTGCGGGCGTCCTAAAGGTCTTGCTGACCTGTGCG‑GGCGGTCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGTTCGATATCGTc  <  2:48474/142‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                             
TTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTC  >  CP009273/468007‑468284

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑