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
A14 F56 I20 R2 1958 92.1 3575798 91.1% 3257551 126.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP006881 3,725,237 A→G intergenic (‑69/‑460) U712_19205 ← / → U712_19210 Uncharacterized protein ywcI/Minor extracellular protease vpr

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,725,2370AG80.0% 105.8 / 2.4 55intergenic (‑69/‑460)U712_19205/U712_19210Uncharacterized protein ywcI/Minor extracellular protease vpr
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (31/13);  minor base C (0/11);  total (31/24)
Fisher's exact test for biased strand distribution p-value = 2.09e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑C‑TTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAGAAG  >  CP006881/3725114‑3725366
                                                                                                                                 |                                                                                                                                 
cccAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGc                                                                                                                     >  7:364862/1‑139 (MQ=255)
          caAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtttcttt                                                                                                           >  8:50528/1‑139 (MQ=255)
                 acaaTCAACACCGGTAAATATACAAGCAACCGTTTAATACAAAAACATCCCTCCGCTTCTTTTTGGCTGCCCG‑CGT‑TTTT‑C‑GCCGCCG‑GTTTTCTCCGCCGCACCCCGAAATAAACCACGGCCGATTTCTTTTCTCGCa                                                                                                    <  6:381308/136‑1 (MQ=255)
                 aCCATCCACACCCTTAAAGATACAAGCAAACGTATCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑TTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCa                                                                                                    <  5:393379/139‑1 (MQ=255)
                   cATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCACCCCCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTATCGCaa                                                                                                   >  7:336810/1‑138 (MQ=255)
                    aTCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCCGCCCGCAAGAAAAGACGGCCGATTTCGTTTCTCGCaaa                                                                                                  >  5:381308/1‑138 (MQ=255)
                    aTCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATATCATTTCTCGCaaa                                                                                                  >  7:115057/1‑138 (MQ=255)
                       cacacaCGAAAAGAAACACCAAAACGTTTCATAAAAAAACATCCCTCCGGTTGTTTTGGCCTGGCAG‑C‑CTTTTT‑T‑GCCGCCG‑GTTTCCTCCGCCGCCGCCCGCTAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAg                                                                                              <  8:50997/139‑1 (MQ=255)
                       cacaCCCGAAAACAACCAACCAAACTTTTCAAACAAAAACATCCCGCCGCTTCTTTTTGGCCGGCCG‑C‑CTTTTT‑A‑GCAGCCG‑GTTTTCACCCCCCCCCCCCCCAATAAAACACGGCCGATTTCTTTTCTCGCAAACTAg                                                                                              <  2:342199/139‑1 (MQ=255)
                            ccGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGct                                                                                         >  4:135490/1‑139 (MQ=255)
                               tAAAGATACAAGCATACGTATAATACAAAAACATCCATCCGCTTCTTTTTGGCAGGCAG‑C‑C‑TTTTAA‑GCAGCAC‑GTTTTCTCAGCCTCAGCCCGCAAGAAAAGCCGGCCGATTTCTATTCTCGCAAACTATCggagc                                                                                        >  7:45758/1‑134 (MQ=255)
                               tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTATTTTATCGCAAACTAGCGGctc                                                                                        >  7:240211/1‑137 (MQ=255)
                               tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACTAGCGGctc                                                                                        >  3:137094/1‑137 (MQ=255)
                                caggaaaCAAGCAAACTTTTCATACAAAAACATCCCTCCGATTTTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCACCCC‑GTTTTCTCAGCCCAAGCCCGCAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAg                                                                                     <  2:40784/133‑1 (MQ=255)
                                aaaGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCATTTTTGCATTCAG‑C‑CTTTTT‑A‑GCAGCCC‑CTATTCACAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTTCCACACAAGCGGcgc                                                                                        >  1:443857/1‑134 (MQ=255)
                                    aTACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCGCTAGCaa                                                                                  >  1:100966/1‑138 (MQ=255)
                                      aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCTG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCATGAAAAGACGGCCGATTTCTTTTCTGGCAAGAGAGGGGGTCTAGCATAAc                                                                               >  4:85899/1‑139 (MQ=255)
                                      aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCCGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTAGCAAACAAGCCGCGCAAGCaaaa                                                                                >  1:191434/1‑138 (MQ=255)
                                      aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCaaaa                                                                                >  5:210093/1‑138 (MQ=255)
                                      aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAAc                                                                               >  7:99741/1‑139 (MQ=255)
                                      aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTACCGGCTCTAGCaaaa                                                                                >  8:48182/1‑138 (MQ=255)
                                      aCAAGCAAACGTTTCATAGAAAAACATCCATCCGCTTATTTTTGGCAGGCAG‑C‑CATTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAATACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCGAGCaaaa                                                                                >  7:143201/1‑138 (MQ=255)
                                      aCAAGCAAACGTATCATAGAAAAACATCCCTCCGCTTCTTTTAGGCAGGCAGAC‑T‑TTTT‑A‑GCATCCA‑GGTTTCTCAGCCGCAGCCCGCAAGAAAAGACCGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGGAAAAc                                                                               >  8:130539/1‑139 (MQ=255)
                                          gCAAACTTTTAATACAAAAACACCCCACCCCTTATTTTTGCCCGGCAG‑CAT‑TTTT‑A‑CCCGCCC‑TTTTTGGCCGCCGACCCCCGAAACAAACGACGGCCGTTTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                           <  6:194801/139‑1 (MQ=255)
                                          gCAAACGTTTCATAGAAAAACATCCCACCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                           <  7:74170/139‑1 (MQ=255)
                                          ccAACCGTTTCATAGAAAAACATCCCACCGCTTCTTTTTGGCAGGCCC‑C‑CTTTTT‑C‑GCAGCCG‑GTTTTCTCCCCCGCAGCCCCAAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                           <  7:50528/138‑1 (MQ=255)
                                          ccAAACGTTTCATATAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑A‑TTTTAA‑GCAGCCC‑GTTTTCTCCGCCGCACCCGGAAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                           <  3:439279/138‑1 (MQ=255)
                                          caaaaCGTTTCATACAAAACCAGCCCCCCGCTTCTTTTTGCCAGGCCG‑C‑C‑TTTT‑ACCCCGCCC‑GTTTCCCCCGCCCCCCCCCCAAACAACACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                           <  1:392233/137‑1 (MQ=255)
                                            aaaCTTTTAAAAGAAAAACAACCCTCCGCTTCTTTTTGGCAGGCAG‑CAT‑TTTT‑C‑GCAGCCG‑GTTTTCTCCGCCCCAGCCCGAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa                                                                         <  8:99741/139‑1 (MQ=255)
                                            aaaCGTTTCATATAAAAAGACCCATCCGATTCTTTGTCGCCGGCAG‑C‑CTTTTT‑A‑CGCGCCG‑GTTTCCACCGCCGCACCCCCCAAGAAATCACGGCGGATTTCTTTTCTCGAAAACAAGCGGCTCTAGCAAAACTCATGa                                                                         <  4:225585/139‑1 (MQ=255)
                                            aaaCGTTTAATACAAAAACAACCCTCCGCTTATTTTGGGCCGCCAG‑CTT‑TTTT‑C‑CCAGCCC‑GTTTTCTCAGCCGCCCCCCGAAAAAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa                                                                         <  2:46075/139‑1 (MQ=255)
                                              actttacATACAAAAACAGCCCTCCGCTTATTTTTGGCAGGCTG‑C‑T‑TTTT‑ACGCCGCCC‑GTTTTCTCCGCCGCAGCCCGCAACAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                       <  6:225751/133‑1 (MQ=255)
                                              aCGTTTCATCCAAACACCGCCCGCCGCTTCTTTTTGGCAGGCAG‑CGT‑TTTT‑C‑GCCGCCC‑GTTTGCCCCGCCCCCCCCCCCAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                       <  3:116517/139‑1 (MQ=255)
                                              aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATgctg                                                                       >  1:40784/1‑136 (MQ=255)
                                              aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                       <  6:210093/139‑1 (MQ=255)
                                              aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                       >  7:51888/1‑139 (MQ=255)
                                              aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCCCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                       <  7:261366/139‑1 (MQ=255)
                                              aCGTTTCAAACAAAAACAACCCTCCGCTTCTTTTTGGCAGGCAG‑C‑C‑TTTTAA‑GCAGCCC‑GTTTTCTCCGCCCCCCCCCCCAACAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                       <  2:35968/139‑1 (MQ=255)
                                              aCGTATCATATAAAAACATCCCCCCGCTTCTTTTTGGCAGGCAG‑CGT‑TTTT‑C‑GCAGCCG‑GTTTTCTCCCCCGCAGCCCGCAAGAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                       <  1:99729/139‑1 (MQ=255)
                                                    cATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCACAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCCGCTCTAGCAAAACACATTAcact                                                                     >  5:72708/1‑135 (MQ=255)
                                                       aGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCCAACTAGCGGCTCTAGCAAAACTCCTGCCTCGATGATAg                                                              >  2:294139/1‑139 (MQ=255)
                                                         aaaaaCATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTACTCAGCCGCAGCCCCCAAGAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGAc                                                            <  7:2398/139‑1 (MQ=255)
                                                               aTCCCCCCGCTTTTTTTGGCCCGGCAG‑CTT‑TTTT‑C‑GCAGCCG‑GTTTTCCCCCCCCCCGCCCCAAAAAAAACACGGCCGATTTCTTTTCTCGAAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGa                                                      <  1:158139/139‑1 (MQ=255)
                                                                  ccTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGCCTCTATGATAGACCGTGGa                                                      >  2:126799/1‑136 (MQ=255)
                                                                          tcttTTTGGCCGCCCC‑C‑C‑TTTT‑T‑CCCCCCCGGTTTTCTCAGCCGCACCCCGAAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCt                                           <  7:12099/139‑1 (MQ=255)
                                                                           cttTTTGGCAGGCAG‑C‑CGTTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACCGCCGATTTCTTTTCTCGCAAACAAGCGGCTCGAGCAAAACGCATTACACTATTATATCCCGGGGAAATAGAattatt                                          >  8:187965/1‑139 (MQ=255)
                                                                               ttGGCAGGCCG‑C‑CTTTTT‑C‑GCCCCCC‑GTTTCCTCAGCCCCCCCCCCCAACAAACCACGGCCGATTTCTTTTCTCGCAGACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGt                                       <  7:116752/138‑1 (MQ=255)
                                                                                                   tttccagcCG‑TTTTTCTCAGCCCCCGCCCCAAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGaaa                       <  4:97768/134‑1 (MQ=255)
                                                                                                          ccc‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTTGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCaa                >  3:97768/1‑138 (MQ=255)
                                                                                                          ccc‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAaacaac               >  5:333108/1‑139 (MQ=255)
                                                                                                          ccc‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGAAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAAc               >  2:74867/1‑139 (MQ=255)
                                                                                                            c‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCACAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCAGAATATGAGTGAAAAAACCAACTa             >  4:377004/1‑139 (MQ=255)
                                                                                                            c‑GTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGCCCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAAc               >  6:250913/1‑137 (MQ=255)
                                                                                                                      aGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAg     >  7:332240/1‑138 (MQ=255)
                                                                                                                        ccGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGCCCGTGGAAAGAGAATTCTTTGTCACAAAATGAGTGAAAAAACCAACTAGTTTTTAGAAg  >  8:381209/1‑139 (MQ=255)
                                                                                                                                 |                                                                                                                                 
CCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑C‑TTTT‑A‑GCAGCCC‑GTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAGAAG  >  CP006881/3725114‑3725366

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