Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 3,960,035 C→A 19.0% R87S (CGC→AGC)  rho → transcription termination factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092733,960,0350CA19.0% 51.7 / 5.5 31R87S (CGC→AGC) rhotranscription termination factor
Reads supporting (aligned to +/- strand):  ref base C (13/12);  new base A (4/2);  total (17/14)
Fisher's exact test for biased strand distribution p-value = 6.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.14e-01

CATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGCAACAAAATCCTCTTTGAGAACT  >  CP009273/3959887‑3960182
                                                                                                                                                    |                                                                                                                                                   
cATCCTGCAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATcc                                                                                                                                                     <  1:164162/149‑1 (MQ=255)
     tGAAGCAGCACGCAAAGAGTGGCGAAGCTATATTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGTATTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGCCATCTCCGCTTCCCCTAGCCAAATCCGCAGt                                                                                                                                                >  2:261030/1‑149 (MQ=255)
     tGAAGCAGCACGCAAAGAGTGGCGAAGATAGCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTGGCCAAATCAGCCGt                                                                                                                                                >  1:168722/1‑149 (MQ=255)
             caCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCt                                                                                                                                        >  2:19544/1‑149 (MQ=255)
             caCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTCCCCCTAGCCAAATCCGCCGTTTCAACCt                                                                                                                                        >  2:19381/1‑149 (MQ=255)
               cGCAAAGAGTGGCGAAGATATCTTTGCCAAAGGCGTACTAGAGATATTGCAGGATGGATTTGGTTTCCGCCGTTCCGCAGACAGCGCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCAGCCGTTTCAACCTcc                                                                                                                                      >  2:189681/1‑149 (MQ=255)
                          gCGAAGATATCTTTGGTGATGGCGTACTGGATATATTGCAGGATGGATTTTGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGAt                                                                                                                           <  1:219503/149‑1 (MQ=255)
                          gCGAAGATACCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTTGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGAt                                                                                                                           <  1:182561/149‑1 (MQ=255)
                            gAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTAGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCAGCCGTTTCAACCTCCGCACTGTTGATAc                                                                                                                         >  1:168573/1‑149 (MQ=255)
                                    cTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTg                                                                                                                 >  2:263924/1‑149 (MQ=255)
                                         gggATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAg                                                                                                            <  1:273519/147‑1 (MQ=255)
                                              gggcgaCTGGGGGTCTTGCAGGAGGGTGTTGGTTGCCTCCGGTGCGCAGGCAGCTGCGACCGCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTcg                                                                                                       <  2:317207/144‑1 (MQ=255)
                                                        agaTATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCCCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGaaa                                                                                             >  2:5011/1‑149 (MQ=255)
                                                                              tttCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGATTCCCCTAGCCAAATCCGCAGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCACCGAAAGAAGGTGAACGCTATTTTgcgc                                                                       >  1:121115/1‑149 (MQ=255)
                                                                                  ctccGTTCCGCAGACAGCTCCTCCCTCGCCGGTCCTGAAGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGACAGACGGGGAACGCTATGTTGCgctgct                                                                   >  1:81506/1‑149 (MQ=255)
                                                                                  ctccGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTACAAACATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCGGGTGAGAATCGCCCGCCTAAAGAAGAGGAACGCTATATTGCgctgct                                                                   >  1:104160/1‑149 (MQ=255)
                                                                                       ttCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCGATTTTGCGCTGCTGaaaa                                                              >  2:282099/1‑148 (MQ=255)
                                                                                         ccGCAGCCGCCTCCTACCCCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCCCCGCACCGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGtt                                                            <  2:21059/149‑1 (MQ=255)
                                                                                                ccgCTCCTACCTCGCCGGTCCTGAGGACATCTACCTTTCCTCTACCCAATGCCGCCGTTTCAACCCCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAg                                                     <  2:184631/147‑1 (MQ=255)
                                                                                                catcTCCTGCCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAACTCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGGTGACGAAg                                                     <  2:201564/146‑1 (MQ=255)
                                                                                                cAGCTCCTACCTCGCCGGTCCTTATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTCGTAAGATTCGCCCGCCGAAAGAAGGTGAAAGCTATTTTGCGCTGCTGAAAGTTAACGAAg                                                     <  2:66579/149‑1 (MQ=255)
                                                                                                cAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCTCGCCGAAAGAAGGTGAAAGCTATTTTGCGCTGCTGAAAGTTAACGAAg                                                     <  1:228866/149‑1 (MQ=255)
                                                                                                            cGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGGAGGTGAACGCTATTTTGCGCTGCGGACAGTTAACGAAGTTAACTTCGaga                                         >  2:209527/1‑147 (MQ=255)
                                                                                                              ccGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAATGTTTTTTTGCGCTGCTGAAAGTGAACGAAGTTAACTTCGACaaa                                       <  1:19651/149‑1 (MQ=255)
                                                                                                                 gTCCTGATGACATCTACGTTTCCCCTAGCCAAATCAGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACCAACCt                                    >  1:266266/1‑149 (MQ=255)
                                                                                                                    cTGATGACATCTACGTTTCCCCTGGCCAACTCAGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGaa                                 <  2:168722/149‑1 (MQ=255)
                                                                                                                                    ttCCCCTAGCCAAATCAGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGCAACaaaa                 <  1:189681/149‑1 (MQ=255)
                                                                                                                                           aGCCAAATTCGCCGTGTCAAACTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAAAGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGCAACAAAATCCTCtt          >  2:252230/1‑149 (MQ=255)
                                                                                                                                             ccAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGATAACGAAGTTAACTCCGACAAACCAGAAACCGCCAGCAACAAAAACACCTTTg        >  2:291793/1‑149 (MQ=255)
                                                                                                                                               aaaTCCGCCGTTTCAACCTCCGCCCTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGGAAACGCCCGCAACAAAGTCCTCTTTgag      >  1:277682/1‑149 (MQ=255)
                                                                                                                                                  tCCGCCGTTTCACCCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGATGTTAATTTCGACAAACCTGAAAACGCCCGCAACAAAATCCTCTTTGAGAAc   <  1:19381/149‑1 (MQ=255)
                                                                                                                                                  tCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTTTCGTTGTTTATTTTGACAAACCTGAAAACGCCCGCAACAAAATCCTCTTTGAGAAc   <  1:19544/149‑1 (MQ=255)
                                                                                                                                                   ccgccgTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGATATTTTGCTCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGCAAGAAAATCCTCTTTGAGAACt  >  1:41231/1‑149 (MQ=255)
                                                                                                                                                    |                                                                                                                                                   
CATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGCAACAAAATCCTCTTTGAGAACT  >  CP009273/3959887‑3960182

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: ‑