Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A11 F58 I0 R3 223 82.2 2922920 95.2% 2782619 126.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 1,672,787 G→T 21.8% M1M (ATG→ATT) † U712_08615 → Flagellar biosynthesis protein flhF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068811,672,7870GT21.8% 85.5 / 7.7 56M1M (ATG→ATT) †U712_08615Flagellar biosynthesis protein flhF
Reads supporting (aligned to +/- strand):  ref base G (21/21);  new base T (10/2);  total (32/24)
Fisher's exact test for biased strand distribution p-value = 5.12e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCTCGCCGCCTGTCAGAATGTATGTGAAGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTGGCCTCGTCAACAAGCC  >  CP006881/1672657‑1672921
                                                                                                                                  |                                                                                                                                       
tGCTCGCCGCCTGTCAGAATGTATGTGAAGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATAGGAGTGGTGGATATTTAATTAAAAT‑aa                                                                                                                                 >  4:361712/1‑138 (MQ=255)
  cTCGCCGCCTGTCAGAATGTATGTGAAGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑aaaa                                                                                                                               >  5:340198/1‑138 (MQ=255)
                gAATGTATGTGAAGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTgctgct                                                                                                                <  2:244912/139‑1 (MQ=255)
                     tatgtGAAGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAAt                                                                                                           >  6:339133/1‑139 (MQ=255)
                     tatgtGAAGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTAATTCTTCTTCAAt                                                                                                           >  6:172686/1‑139 (MQ=255)
                       tgtgAAGCAGCTACTGGACCGGTACTTCCCTGAGGTTCCGGTAGTCTCTTATAACGACCTTGAGGCGAATGTTGAGGTACAGAGCATTGGAGTGGGGGAGTTTTTATGTAATT‑TAAAACAGTTTCTGGTGGTGCAATg                                                                                                          >  2:53104/1‑138 (MQ=255)
                           aaGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGTTATTTAATTAAAAT‑AAAAAAATTTAATGGTGCTTCaaagaaag                                                                                                      >  3:157308/1‑138 (MQ=255)
                           aaGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGGTTTTTTATGAAAAT‑AAAAAAATTTAATGATGCTTGAATGc                                                                                                         >  5:222515/1‑135 (MQ=255)
                           aaGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCaaga                                                                                                     <  2:52050/139‑1 (MQ=255)
                           aaGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCa                                                                                                        <  4:260271/136‑1 (MQ=255)
                           aaGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCa                                                                                                        >  3:260271/1‑136 (MQ=255)
                                 cTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATTAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGc                                                                                               >  1:286709/1‑139 (MQ=255)
                                 cTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCgg                                                                                                <  5:262111/138‑1 (MQ=255)
                                 cTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCgg                                                                                                >  6:262111/1‑138 (MQ=255)
                                          cGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCtcat                                                                                      <  5:339133/139‑1 (MQ=255)
                                          cGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCtcat                                                                                      <  5:172686/139‑1 (MQ=255)
                                              aCTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGGTATTTTATTAAAAT‑AAAAAAATTTTATGCTGCGTGAATGCAAGGAGCGGCCCGTCtcatcct                                                                                   >  6:309440/1‑136 (MQ=255)
                                                    cTGATCTTACGGTACTCTCTTATAACGAACTGGAGGCGAGTGTTTAGGGACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAagag                                                                            <  6:133861/139‑1 (MQ=255)
                                                      agacagccGTTACTCTATTATAACGAACTTGAGGCTAATGTTGAGGTAAAAAGAATTGGAGTGGTGTATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGtt                                                                          <  4:286984/133‑1 (MQ=255)
                                                       atattgcGGTATTGTCTTATAACGAACTTGAGGCGATTGTTGAGGTACAAAGCATTGTAGTTGTGTATATTTAATTAAATT‑AAAATAATTTACTGCTTCTTCAATGCAAGTAGCGGCACTTCTCATCAGAAAAGTGtt                                                                          <  6:270984/132‑1 (MQ=255)
                                                       agcTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGTATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGtt                                                                          <  6:41535/136‑1 (MQ=255)
                                                       accTTCCGGTACACTCTTATAACGAACTTCCGGCTAATGTTGCGGTACAAAGCATTGGAGTGGGGGATATTTAATTAAAAT‑AAAAAAATTAACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGtt                                                                          <  6:36637/136‑1 (MQ=255)
                                                       aTCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATTAAAAT‑AAAAAAATTTAATGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTa                                                                         >  3:26578/1‑139 (MQ=255)
                                                       aTCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGtt                                                                          <  3:147567/138‑1 (MQ=255)
                                                       aTCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑‑AAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGtt                                                                          <  3:310883/137‑1 (MQ=255)
                                                       aTCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATATAAAAAAAAA‑AAAAAAAATTACAGCTGCATCAATGATACAAGCCCCACAACTCGACAGAAAAAAGTTa                                                                         >  5:62809/1‑139 (MQ=255)
                                                            ccGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTa                                                                     <  8:6862/138‑1 (MQ=255)
                                                             cGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTAAAGCTGCTTCAATGCAAGAAGCGGCACGTCTCATCAGAAAAGAGTTAGGTAAt                                                                   >  3:288468/1‑139 (MQ=255)
                                                              ggTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAAt                                                                   >  3:328586/1‑138 (MQ=255)
                                                               gTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGa                                                                 <  6:340198/139‑1 (MQ=255)
                                                                  ctctctTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCTTTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAg                                                               <  3:361712/138‑1 (MQ=255)
                                                                  ctctctTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAg                                                               <  5:359714/138‑1 (MQ=255)
                                                                       ttATATCGAACTTGAGGTGAATGTTGATGTACAAAGCATTGGAGTGGTGGTTTTTTAATGAATAT‑AAAAAAATTTACTGCTGCTTCAATGAAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGt                                                           <  4:157308/137‑1 (MQ=255)
                                                                       ttATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGTTATTTTTTTAAAAT‑AAAAAAATTTTAAGCTGCTTCAATGCAATAACCGGCGCTTCTCATCAGAAAATAGTTAGGTTATGAAGCgggga                                                         >  5:316453/1‑136 (MQ=255)
                                                                       ttATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGTTATTTAAATAAAATAAAAAAAATTTAAT‑CTGCTTAAATGCAAGAAGCGGCACTTCTCAAAATAAAAGAGTTATGTTATGAAGctgg                                                           >  3:286984/1‑134 (MQ=255)
                                                                         ataACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGt                                                           <  4:328586/135‑1 (MQ=255)
                                                                          taACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTAATGCTGCTTCAATGCAAGAAGCGGCACTTGTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCatat                                                      >  2:252679/1‑139 (MQ=255)
                                                                               aaCTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGTTATTTTATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAATCGGGCCTTCTCATCAGATAAGATTTATGTAATTAAGCGGTCAAATTAAAt                                                 >  4:45127/1‑139 (MQ=255)
                                                                               aaCTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTATCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAAt                                                 >  7:296828/1‑139 (MQ=255)
                                                                                 cTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATTAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCAAATCAGAAAATAGTTTGGTAATGAAGCGGTCATATTAAAt                                                 >  1:118995/1‑137 (MQ=255)
                                                                                 cTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑TAAAAAATTTTATTCTGCTTCTATGCAAGAAGCGGCACTTGTGATCTGAAAAGAGTTATGTTATGTAGCGGTCATATTAAATTc                                               >  6:130052/1‑139 (MQ=255)
                                                                                 cTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCTTCAGAAAAGAGTTAGGTAATGAAGCGGGCATATTAAATTc                                               >  7:155423/1‑139 (MQ=255)
                                                                                          aaTGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCAAATTAAATTCGAAAAAAAt                                      >  2:73531/1‑139 (MQ=255)
                                                                                          aaTGTTGAGGTACAAAGCATTGGAGTGGTGGATAATTTATTATTAT‑AAAAAAATTTTATGCAGCTTCAATTCAAGAAGCGGCAAATATCAACATAAAAGACATAGGGAATTAAGCGGTGATATTAAATTAGAAAAAAAt                                      >  1:243898/1‑139 (MQ=255)
                                                                                            tGTTGAGGTACAAAGCATTGGAGTGGTGGGTATTTAATTAAAAT‑AAAAAAATTTTCTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTTATGAAGCGGTCATATTAAATTCGAAAAAAAtt                                     >  5:27762/1‑138 (MQ=255)
                                                                                                      aaaaGCATTGGAGTGGTTGATATTTAATCAAAAT‑AAAAAAATTTAATGATGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGaaa                          <  5:315998/138‑1 (MQ=255)
                                                                                                           cATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGt                     >  5:180279/1‑139 (MQ=255)
                                                                                                              tGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGATTTAGGTAATGAAGCGGGCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTg                  >  2:12080/1‑139 (MQ=255)
                                                                                                              tGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTg                  >  7:179286/1‑139 (MQ=255)
                                                                                                              tGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACAGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTTGGGAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAAAGGTTTg                  >  5:340356/1‑139 (MQ=255)
                                                                                                                caggggtgcATATTTAATGAAAAA‑AAAAAAATTTACGGCTCCTTCAAGGCAAGCCGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAACGCGAAAATGGTTTGGc                <  6:316453/135‑1 (MQ=255)
                                                                                                                   tggtggATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTGGCCTc             <  1:252679/139‑1 (MQ=255)
                                                                                                                     gtggATATTTTATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGGCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTGGCCGCGt           >  4:20964/1‑139 (MQ=255)
                                                                                                                               aaTGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAagag                                                                            <  1:136636/64‑1 (MQ=255)
                                                                                                                               aaTGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAagag                                                                            >  2:136636/1‑64 (MQ=255)
                                                                                                                               aaTGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTGGCCTCGTCAACAAGcc  <  1:12080/138‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                       
TGCTCGCCGCCTGTCAGAATGTATGTGAAGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAAT‑AAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTGGCCTCGTCAACAAGCC  >  CP006881/1672657‑1672921

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A