Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 1,294,949 T→C 7.5% L57P (CTC→CCC)  U712_06580 → Phage‑like element PBSX protein xkdJ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068811,294,9490TC 7.5% 151.1 / 4.0 55L57P (CTC→CCC) U712_06580Phage‑like element PBSX protein xkdJ
Reads supporting (aligned to +/- strand):  ref base T (26/24);  new base C (2/2);  total (29/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.59e-01

CCGGTGGTCTGTTCCCATTTATGAACGCGAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGCGAGAAGACGGGGGATATGGTTCGCAT  >  CP006881/1294821‑1295087
                                                                                                                                |                                                                                                                                          
ccGGTGGTCTGTTCCCATTTATGAACGCGAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCAACTGTTTTGGAGGAAAAAGATACGGTGTCCACATTTAAAAAAACATACAGTCTCATtgtgc                                                                                                                                    >  5:28455/1‑136 (MQ=255)
    tggtCTGTTCCCATTTATGAACGCGAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGt                                                                                                                              <  6:203245/139‑1 (MQ=255)
    tggtCTGTTCCAATTTATGAACGCGAGCTTCCTGATCACTTTCATGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGGCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGt                                                                                                                              <  2:131136/139‑1 (MQ=255)
          gTTCCCATTTATGAACGCGAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGCTACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATc                                                                                                                        >  3:176303/1‑139 (MQ=255)
                aTTTATGAACGCGAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACt                                                                                                                  >  6:190337/1‑139 (MQ=255)
                aTTTATGAACGCGAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACt                                                                                                                  <  5:190337/139‑1 (MQ=255)
                 tttATGAACGCGAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTc                                                                                                                 >  3:93662/1‑139 (MQ=255)
                   tATGAACGCGAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGtct                                                                                                                                            >  7:210062/1‑110 (MQ=255)
                   tATGAACGCGAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGtct                                                                                                                                            <  8:210062/110‑1 (MQ=255)
                         cgcgAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAgg                                                                                                         >  1:153275/1‑139 (MQ=255)
                         cgcgAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCAACTGTTTTCGAGGAAACAGATACTGTCTCCACATTTAAAAAAACCTACAGTCACAATGTGAAACTGTTTCATCGTGACTCCGATCAgg                                                                                                         >  8:348009/1‑139 (MQ=255)
                          gcgAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGgc                                                                                                        >  5:259518/1‑139 (MQ=255)
                           cgAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGgcg                                                                                                       <  5:57314/139‑1 (MQ=255)
                           cgAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGgcg                                                                                                       <  5:188628/139‑1 (MQ=255)
                           cgAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGgcg                                                                                                       <  6:109804/139‑1 (MQ=255)
                                  ccTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGa                                                                                                  <  6:259518/137‑1 (MQ=255)
                                      aTCACTTTCAGGAGCCGTCGTTATATGACCCGCCACCATCTGTTATCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGaa                                                                                              <  5:251548/137‑1 (MQ=255)
                                         aCTTTCAGGTGCCGTCGATATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTAAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGa                                                                                         <  1:55848/139‑1 (MQ=255)
                                             tCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAg                                                                                      <  2:153275/138‑1 (MQ=255)
                                                    ccGTCGTTATATGTCCCGCCCCCATCTGTTTTCGCGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCgg                                                                              >  8:134200/1‑139 (MQ=255)
                                                    ccGTCGTTATATGTACCGCCACCATCAGTTTTAGAGGAAACAGATACGGGCTCCACATTTAAAAAACCCTACAGTCTCAATGTGCAACTGTTTCATCTGGCCTCCGTTCAGGCGCTGGATGCAGCGGCCAGGCTCGCgg                                                                              >  1:292579/1‑139 (MQ=255)
                                                     cgtcgtTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGa                                                                             >  1:19067/1‑139 (MQ=255)
                                                     cgtcgtTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAAATACGGTAACCACAATTAAAAAAACCTACAGTCTCAAAGTGAAACTGTTTCCTCTGGACTCCGTTGAGGCGCTGGATGAAGCGGACAGGCTCGCGGa                                                                             >  5:316029/1‑139 (MQ=255)
                                                         gtTATATGTCCCGCGACCATCTGTTTCCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGc                                                                          <  1:174303/138‑1 (MQ=255)
                                                                 tCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTGAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAgaga                                                                 <  2:298202/139‑1 (MQ=255)
                                                                 tCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCagag                                                                  >  5:385868/1‑138 (MQ=255)
                                                                  cccGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGtct                                                                                                                                            <  7:281047/63‑1 (MQ=255)
                                                                  cccGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGtct                                                                                                                                            >  8:281047/1‑63 (MQ=255)
                                                                   ccGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAg                                                               >  1:66743/1‑139 (MQ=255)
                                                                    cGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGc                                                              >  1:98402/1‑139 (MQ=255)
                                                                       caccaTCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTcgcg                                                                               >  4:209394/1‑119 (MQ=255)
                                                                       caccaTCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTcgcg                                                                               <  3:209394/119‑1 (MQ=255)
                                                                       caccaTATGTTTTCGAGGAAACAGATACGGGCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCGGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCgag                                                           <  6:180756/139‑1 (MQ=255)
                                                                            tCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAata                                                      >  6:192137/1‑139 (MQ=255)
                                                                                ttttCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGAt                                                  >  7:384815/1‑139 (MQ=255)
                                                                                  ttCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTc                                                >  7:308514/1‑139 (MQ=255)
                                                                                   tCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAATCTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTc                                                <  3:250428/138‑1 (MQ=255)
                                                                                   tCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTc                                                <  8:384815/138‑1 (MQ=255)
                                                                                            cAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAg                                      <  7:134200/139‑1 (MQ=255)
                                                                                                   ggTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATcc                               >  8:306024/1‑139 (MQ=255)
                                                                                                    gTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCg                              <  4:93662/139‑1 (MQ=255)
                                                                                                      ctcCACATTTAAAAAAACCTACAGTCCCAATGTGAACCTGTTTCATCTGGACTCCGGTCCGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGc                            <  3:363997/139‑1 (MQ=255)
                                                                                                       tcCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCTGAGAAGCGAGAAATATGATTCCGCTGGTGAGTGAATCCgggg                           >  2:160774/1‑137 (MQ=255)
                                                                                                       tcCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGc                            >  6:377915/1‑138 (MQ=255)
                                                                                                       tcCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGc                            >  7:244585/1‑138 (MQ=255)
                                                                                                         cacaTTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGc                            >  5:127969/1‑136 (MQ=255)
                                                                                                         cacaTTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGc                            >  7:315444/1‑136 (MQ=255)
                                                                                                         cacaTTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGc                            >  3:107157/1‑136 (MQ=255)
                                                                                                             tttAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGCGagaaga                     >  1:77495/1‑139 (MQ=255)
                                                                                                              ttAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGa                                                                                         <  2:401169/70‑1 (MQ=255)
                                                                                                              ttAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGa                                                                                         >  1:401169/1‑70 (MQ=255)
                                                                                                               tAAAAACACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGAGGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGCGAGAAGAc                    <  7:152682/138‑1 (MQ=255)
                                                                                                               tAAAAACACCTACAGTCCCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGAGGCCATCAGAGAAGCGAGAAAGATGATTCCGCTGCTGAGTGAATCCGTCGAGacgacg                   >  4:363997/1‑139 (MQ=255)
                                                                                                               tAAAAAAACCTACAGTCCCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGc                            <  3:363999/130‑1 (MQ=255)
                                                                                                               tAAAAAAACCTACAGTCCCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGc                            >  4:363999/1‑130 (MQ=255)
                                                                                                                aaaaaaaCCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGCGAGAAGACg                   <  5:192137/138‑1 (MQ=255)
                                                                                                                     aaCCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGCGAGAAGACGGGGGat             <  8:244585/139‑1 (MQ=255)
                                                                                                                           cAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGCGAGAAGACGGGGGATATGGtt       <  2:77495/139‑1 (MQ=255)
                                                                                                                           cAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGCGAGAAGACGGGGGATATGGt        <  1:268801/138‑1 (MQ=255)
                                                                                                                              tctcTATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGATAAATATGATTCCGCTGCTGAGTGAATCCGGCGAGAAGACGGGGGATATGGTTCGc    <  7:348009/139‑1 (MQ=255)
                                                                                                                                tcAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGCGAGAAGACGGGGGATATGGTTCGCAt  >  7:398152/1‑139 (MQ=255)
                                                                                                                                tcAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGCGAGAAGACGGGGGATATGGTTCGCAt  >  1:237187/1‑139 (MQ=255)
                                                                                                                                |                                                                                                                                          
CCGGTGGTCTGTTCCCATTTATGAACGCGAGCTTCCTGATCACTTTCAGGTGCCGTCGTTATATGTCCCGCCACCATCTGTTTTCGAGGAAACAGATACGGTCTCCACATTTAAAAAAACCTACAGTCTCAATGTGAAACTGTTTCATCTGGACTCCGTTCAGGCGCTGGATGAAGCGGACAGGCTCGCGGATGCCATCAGAGAAGCGAGAAATATGATTCCGCTGCTGAGTGAATCCGGCGAGAAGACGGGGGATATGGTTCGCAT  >  CP006881/1294821‑1295087

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑