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
A7 F1 I2 R1 766 64.2 3232166 90.9% 2938038 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,330,357 +T coding (1395/1434 nt) dacB → D‑alanyl‑D‑alanine carboxypeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,330,3531.T98.3% 191.8 / ‑4.0 60coding (1391/1434 nt)dacBD‑alanyl‑D‑alanine carboxypeptidase
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base T (27/32);  total (28/32)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGGTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑G‑TTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAGTCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATC  >  NC_000913/3330229‑3330485
                                                                                                                              |                                                                                                                                    
ggggTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCTTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  2:1077432/139‑1 (MQ=255)
ggggTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  1:173706/139‑1 (MQ=255)
ggggTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  2:234436/139‑1 (MQ=255)
          aCCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         >  1:458216/1‑129 (MQ=255)
          aCCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         >  1:476631/1‑129 (MQ=255)
          aCCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  2:458216/129‑1 (MQ=255)
          aCCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  2:476631/129‑1 (MQ=255)
              ggCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATaa                                                                                                                 <  1:1107641/133‑1 (MQ=255)
              ggCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATaa                                                                                                                 >  2:1107641/1‑133 (MQ=255)
              ggCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGatat                                                                                                           >  1:1105552/1‑139 (MQ=255)
                cGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         >  2:82490/1‑123 (MQ=255)
                cGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  1:82490/123‑1 (MQ=255)
                cGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATAttt                                                                                                         >  2:1204582/1‑139 (MQ=255)
                  ggATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTAt                                                                                                       <  1:2639/139‑1 (MQ=255)
                               caGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGtat                                                                                                                   >  1:104608/1‑114 (MQ=255)
                               caGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGtat                                                                                                                   <  2:104608/114‑1 (MQ=255)
                                agcgagcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATaa                                                                                                                 >  2:734752/1‑115 (MQ=255)
                                agcgagcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATaa                                                                                                                 <  1:734752/115‑1 (MQ=255)
                                agcgagcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTaatc                                                                                         >  1:594745/1‑136 (MQ=255)
                                  cgagcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑G‑tttttgaa                                                                                                                              >  2:1390971/1‑95 (MQ=255)
                                  cgagcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑G‑tttttgaa                                                                                                                              <  1:1390971/99‑5 (MQ=255)
                                    agcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCaaaa                                                                                     >  2:838174/1‑139 (MQ=255)
                                    agcgGGCAACGAATGGCGTTTGTGCAATATC‑TTCTGCCTATGCAGTATAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGG‑TTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCaaaaa                                                                                    >  2:1024123/1‑139 (MQ=255)
                                      cgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAg                                                                                   >  2:794868/1‑139 (MQ=255)
                                      cgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAg                                                                                   >  1:1181595/1‑139 (MQ=255)
                                       gggCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGa                                                                                  <  1:1204582/139‑1 (MQ=255)
                                       gggCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑G‑tttttgaa                                                                                                                              <  2:816384/94‑5 (MQ=255)
                                       gggCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑G‑tttttgaa                                                                                                                              >  1:816384/1‑90 (MQ=255)
                                               aaTGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCgg                                                                          <  2:594745/139‑1 (MQ=255)
                                                  ggCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGcac                                                                       >  1:510083/1‑139 (MQ=255)
                                                   gCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         >  1:601551/1‑88 (MQ=255)
                                                   gCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  2:601551/88‑1 (MQ=255)
                                                   gCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGcaca                                                                      <  2:1503572/139‑1 (MQ=255)
                                                     gTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑G‑tttttgaaa                                                                                                                             <  1:876023/81‑6 (MQ=255)
                                                     gTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑G‑tttttgaaa                                                                                                                             >  2:876023/1‑76 (MQ=255)
                                                          tgCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCgg                                                               <  1:1234999/139‑1 (MQ=255)
                                                            cAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCgggg                                                             <  1:838174/139‑1 (MQ=255)
                                                                       tGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGattat                                                  <  2:510083/139‑1 (MQ=255)
                                                                         gCTATGCAGTAGAACCTGCGGATCAACGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  1:575256/66‑1 (MQ=255)
                                                                         gCTATGCAGTAGAACCTGCGGATCAACGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         >  2:575256/1‑66 (MQ=255)
                                                                             tGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACaa                                            >  1:864898/1‑139 (MQ=255)
                                                                                   aGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTgcg                                      <  2:1105552/139‑1 (MQ=255)
                                                                                    gAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCg                                                                >  2:796492/1‑112 (MQ=255)
                                                                                    gAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCg                                                                <  1:796492/112‑1 (MQ=255)
                                                                                     aaCCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGata                                                                                                            <  2:265471/67‑1 (MQ=255)
                                                                                     aaCCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGata                                                                                                            >  1:265471/1‑67 (MQ=255)
                                                                                     aaCCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGa                                                                                  <  2:678333/93‑1 (MQ=255)
                                                                                     aaCCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGa                                                                                  >  1:678333/1‑93 (MQ=255)
                                                                                       ccTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCttt                                  >  2:1204453/1‑139 (MQ=255)
                                                                                         tGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATaa                                                                                                                 >  1:1191810/1‑58 (MQ=255)
                                                                                         tGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATaa                                                                                                                 <  2:1191810/58‑1 (MQ=255)
                                                                                                cAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCgg                                                               <  1:1499174/101‑1 (MQ=255)
                                                                                                cAGCGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGCCCgg                                                               >  2:1499174/1‑101 (MQ=255)
                                                                                                   cGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTa                                                                                            <  2:729373/69‑1 (MQ=255)
                                                                                                   cGTAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTa                                                                                            >  1:729373/1‑69 (MQ=255)
                                                                                                     tAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATg                    <  1:1024123/139‑1 (MQ=255)
                                                                                                     tAATCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATg                    <  2:864898/139‑1 (MQ=255)
                                                                                                        tCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         >  2:1134202/1‑35 (MQ=37)
                                                                                                        tCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGt                                                                                                                         <  1:1134202/35‑1 (MQ=37)
                                                                                                        tCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAg                                                                                                               >  2:1372688/1‑45 (MQ=38)
                                                                                                        tCGCCGTATTCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAg                                                                                                               <  1:1372688/45‑1 (MQ=38)
                                                                                                                ttCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGca                                                                        >  1:1423618/1‑76 (MQ=255)
                                                                                                                ttCCGTTAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGca                                                                        <  2:1423618/76‑1 (MQ=255)
                                                                                                                     ttAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGa                                                                                  >  1:434817/1‑61 (MQ=255)
                                                                                                                     ttAGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGa                                                                                  <  2:434817/61‑1 (MQ=255)
                                                                                                                       aGTGC‑GTTTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATc  <  1:166526/139‑1 (MQ=255)
                                                                                                                              |                                                                                                                                    
GGGGTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGC‑G‑TTTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAGTCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATC  >  NC_000913/3330229‑3330485

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A