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
A19 F53 I19 R3 125 83.6 3029080 95.4% 2889742 127.2

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
*CP0068813,725,2370AG82.0% 109.8 / ‑0.1 53intergenic (‑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 (30/11);  minor base C (0/9);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 6.70e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑C‑TTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTA  >  CP006881/3725114‑3725355
                                                                                                                                   |                                                                                                                      
cccAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGc                                                                                                          >  4:163093/1‑139 (MQ=255)
     ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTGTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGAtt                                                                                                     >  4:233125/1‑139 (MQ=255)
        atcaAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTATCA‑GCCGCACCCCGCAAGAAAAGACGGCCGAtttat                                                                                                  >  7:11419/1‑137 (MQ=255)
         tcaAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGAtttctt                                                                                                 >  5:143692/1‑139 (MQ=255)
               aGACCATCCACCCCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAATAGACGGCCGAGTTCTTTTCTCg                                                                                           >  6:66262/1‑139 (MQ=255)
               aGACCATCCACACCCGTAAAGATACAAGCAAACCTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑AAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTACTCA‑GCCCCAGCCCGCAAGAAAAGACGTCCGAATTATTTTATCg                                                                                           >  2:213171/1‑139 (MQ=255)
                 cccAACCACCCCCGTAAAGAAACAAGCAACCGTTTCATAGAACACCATCCCTCGGCTTCTTTTTGGCAGG‑CAG‑CGT‑TTTT‑C‑GCCGCCC‑GTTTTCTCC‑GCCGCCCCCCTAACAAAACCACGGCCGATTTCTTTTCTCGCa                                                                                         <  2:210794/138‑1 (MQ=255)
                  ccacccacACCCTTAAACATACAAGCAACCGTTTAATACAAAAACAACCCACCGCTTCTTTTTGGCCGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCC‑GCCGCAGCCCCAAACAAAAGACGGCCGATTTCTTTTCTCGCaa                                                                                        <  3:46258/139‑1 (MQ=255)
                             cGTAAACATACAACCAAACGTTTCATACAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑C‑GCCGCCC‑GTTTTCTCA‑GCCGCCGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc                                                                             <  3:163093/139‑1 (MQ=255)
                               tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTGTCGGAAACGAGCggggg                                                                             >  1:188657/1‑134 (MQ=255)
                               tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc                                                                             >  8:226128/1‑137 (MQ=255)
                               tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc                                                                             >  7:158552/1‑137 (MQ=255)
                               tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAACACGGCCGATTTCTTTTCTCGCAAACTAGAGGctct                                                                            >  8:85165/1‑138 (MQ=255)
                               tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCCCAGCCCGCAAGAAAAGACGGCCGAATTCTTTTCTCGCAAACGAGCGGcgctg                                                                           >  5:260977/1‑138 (MQ=255)
                                aaaGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTGTCGCAAACTAGCGGCTCTAg                                                                          >  1:300683/1‑139 (MQ=255)
                                  ccaTACAAGCAAACGTTTCATACAAAAACATCCCTCCGCTTCTTTTTGGCCGG‑CAG‑C‑CTTTTT‑C‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGAAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa                                                                        <  4:344804/137‑1 (MQ=255)
                                  ataTACAACCATCCGTTTCATATAAAAACATCCCTCCGCTTCTTTTTGGCAGGTTGG‑C‑T‑TTTT‑A‑TCTGCCC‑GTTTTCTCA‑TCCGCACCCCGATAGAAACGACGGCCGATTTCTTTTGTCGCAAAATAGCGGCTCTAGCa                                                                        <  6:181095/137‑1 (MQ=255)
                                    aTACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTGGCAAACTAGCGGCTCTAGCaa                                                                       >  4:53233/1‑138 (MQ=255)
                                      aCAAGCAAACGTTTCATAGAAAAACATCCCTCCTCTTCTTTTTTGCAGG‑CAGAC‑T‑TTTT‑A‑GCATCCC‑GTTTTCTCA‑GACGCAGCCCGCAAAAAAAGACGGCCGATTTGTTTTATAGCAAACTAGCCGCTCTAGCaaaa                                                                     >  7:230317/1‑138 (MQ=255)
                                      aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CCG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCC‑GCCGCCGCCCGCAAGAAAAGACGGCCGAGTTCTGTTCTCCCAAACTAGGGGCTCTTGCAAAAc                                                                    >  6:358422/1‑139 (MQ=255)
                                      aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCCGCCCGCAAGAAAAGACGGCCGAGTTCGTTTCTCGCAAACTAGCGGCTCTGGCAAAAc                                                                    >  8:176547/1‑139 (MQ=255)
                                      aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑ATTTTCTCA‑GCCGCATCCCGCAAGAAAACACGGCCGATTTCTTTTCTCGCAAAAATGCCGCTCAAGCAAAAc                                                                    >  5:181095/1‑139 (MQ=255)
                                        aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTGTTTTTGGCAGG‑CCG‑C‑CTTTTT‑A‑TCAGCCC‑GTTTTCTCC‑GCCGCAGCCCGCAAGAAAAGACGGCCGAAATCAGTTCACGCAAACTAGCGGCTCAAGCAAAACt                                                                   >  6:197602/1‑138 (MQ=255)
                                        aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACt                                                                   >  1:123784/1‑138 (MQ=255)
                                        aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACt                                                                   >  3:249192/1‑138 (MQ=255)
                                          gCAAACGTTTCATATAAAAACAACCCTCCGATTCTTTTGGGCCGG‑CAG‑C‑C‑TTTT‑ACGCAGCCC‑GTTTTCTCC‑GCCCCACCCCGAAACAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                <  6:345956/139‑1 (MQ=255)
                                          ccAACCGTTTCATAGAAAAACAACCCTCCGCTTATTTTTGGCAGC‑CAG‑C‑CTTTTT‑C‑GCAGCCG‑GTTTTCTCC‑GCCGCAGCCCGAAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                <  8:164225/138‑1 (MQ=255)
                                          caaaaCGTTCCAAACAAAACCAGCCTCCCGCTTCTTTTTGGCCGC‑CAC‑C‑G‑TTTT‑A‑CCCCCCCGGTTTCCTCC‑GCCCCACCCCCAAAGAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                <  7:366414/137‑1 (MQ=255)
                                          acAACCGTTCCACACAAAACCATCCCTCCGCTTCTTTTGCGCCGG‑CCG‑C‑CTTTTT‑C‑GCCGCCC‑GTTATCACC‑CCCCCCCCCCCCAAAAACCCCCGGCCGATTGCTTTCCGCCCAAACTCGCGGCTCTAGCAAAACTCAt                                                                <  8:330970/138‑1 (MQ=255)
                                            aaaCGTTCAAAATAAAAACACCCCCCCGCTTCTTTTTGCCTGC‑CCG‑C‑CTTTTT‑C‑GCAGCCC‑GTTTGCCCC‑GCCGCCGCCCCCAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa                                                              <  5:191498/139‑1 (MQ=255)
                                              ccttttCATACAAAAACACCCCTCCGCTCTTTTTGGGCCGG‑CCG‑C‑C‑TTTT‑ACCCACCCC‑GTTTTCTCC‑GCCCCCCCCCCCAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                            <  8:576/136‑1 (MQ=255)
                                              ccgattCATACAAAAACACCCCTCCGCTTTTTTTTGCCTGG‑CCC‑CAT‑TTTT‑A‑CCCGCCC‑GTTTTCTCC‑CCCGCCCCCCCCAACAACACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                            <  4:32083/135‑1 (MQ=255)
                                              ccGTTTCATACAAAACCACCCCGCCGCTTCTTTTTGCCCGC‑CAG‑C‑C‑TTTTAA‑GCAGCCC‑TTTTGCCCC‑CCCGCCCCCCGAAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                            <  5:256086/138‑1 (MQ=255)
                                              ccGTTCCATACAAAAAAATCCCTCCGATTCTTTTTGGCCGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGAAAGAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                            <  7:226128/138‑1 (MQ=255)
                                              aCGTTTCATAGAAAACCACCCCTCCGCTTCTTTTTGGCAGG‑CCG‑C‑CTTTTT‑C‑CCAGCCC‑GTTTCCCCC‑GCCGCCCCCCGAAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                            <  2:214753/139‑1 (MQ=255)
                                              aCGTTTCATACAAAAACATCCCTCCGCTTCTTTTGGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                            <  8:295166/139‑1 (MQ=255)
                                              aCGTTTAATACAAAAACATCCCTCCGCTTCTTTTTGCCAGG‑CAG‑C‑CTTTTT‑C‑GCACCCC‑GTTTTCTCC‑CCCCCACCCCGAAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                            <  7:181449/139‑1 (MQ=255)
                                              aCGTTGAATATAAAAACATCCCGCGGTTTATTTTTGGCAGG‑CCG‑C‑T‑TTTTAA‑GCCCCCG‑TTTTTCTCA‑CCCGCCCCCCCCAACAAACCACGGCCGATTTCTTTTCTCGCAAACTCGCGGCTCTAGCAAAACTCATGAct                                                            <  2:123784/139‑1 (MQ=255)
                                               cGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGActc                                                           >  8:30087/1‑139 (MQ=255)
                                                    aaTAGAAAAACATCCCTCCGCTTCTTTTTGGAAGC‑CAC‑C‑CTTTTT‑A‑CCAGACC‑TTTTTCACA‑CCCGCACCCCTCAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATg                                                       <  7:313822/137‑1 (MQ=255)
                                                           aaaCATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTATAGCAAAATAGCGGCTATAGCAAAACACATGCCTCTATGAAAGACCg                                               >  5:207099/1‑139 (MQ=255)
                                                              cagccccccGCGTGTTTTTGGCTGG‑CAG‑C‑C‑TTTT‑T‑ACCACCC‑CTTTTCGCACGCCCCCGCCCCAAATAAACCACGGCCGATTGCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTgg                                            <  8:265322/136‑1 (MQ=255)
                                                                      cGCTTCTTTTGGGCCGG‑CCG‑C‑CTTTTT‑C‑GCCCCCG‑GTTTGCTCC‑CCCCCAGCCCCAAACAAACGCCGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGaa                                    <  6:143692/139‑1 (MQ=255)
                                                                           cttTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAAGACTCTAAGATAGACCGTGGAAAGAGAATTGtt                               >  4:192131/1‑139 (MQ=255)
                                                                           cttTTTGGCAGG‑CAG‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACCGCCGATTTCTTTTCTCGCAAACTAGCCGCACTAGCAAAACTCAAGACTCTATGAGAGACCGTGGAAAGAGAATTcgt                               >  7:292294/1‑137 (MQ=255)
                                                                           atttttGCCAGG‑CAG‑C‑CTTTTT‑A‑CCCGCCC‑GTTTTCTCA‑GCCCCCGCCCGAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCt                                <  3:192131/137‑1 (MQ=255)
                                                                                      g‑cag‑C‑CTTTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTGTAGCAAAACTAATGACTCTATGATAGACCGTGGAAAGAGAATTCATTGTCTCAatat                    >  4:4649/1‑139 (MQ=255)
                                                                                                         agcCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCCCAATATGAGTGAAAAAAcc       >  3:9075/1‑138 (MQ=255)
                                                                                                          gcCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCaa     >  3:258298/1‑139 (MQ=255)
                                                                                                          gcCC‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACAGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCa      >  6:132753/1‑138 (MQ=255)
                                                                                                           ccc‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTGACAATATGAGTGAAAAAACCaa     >  5:379095/1‑138 (MQ=255)
                                                                                                             c‑GTTTTCTCA‑GCCGCAGCCCTAAATAAATGACGGCCTATTTCTTTTCTCGCAAACTAGAGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTa  <  7:85165/139‑1 (MQ=255)
                                                                                                             c‑GTTTTCTCA‑GCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTATTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATCATAGACCGTGGAAAGAGAATTCTATTTCACAATATCAGAGAAAAAACCAAc    >  6:338767/1‑137 (MQ=255)
                                                                                                                                   |                                                                                                                      
CCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑C‑TTTT‑A‑GCAGCCC‑GTTTTCTCA‑GCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTA  >  CP006881/3725114‑3725355

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A