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 3,528,697 A→C 28.6% A167A (GCT→GCG)  U712_18080 ← Acetolactate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,528,6970AC28.6% 83.1 / 12.4 57A167A (GCT→GCG) U712_18080Acetolactate synthase
Reads supporting (aligned to +/- strand):  ref base A (25/15);  new base C (2/15);  total (27/30)
Fisher's exact test for biased strand distribution p-value = 4.76e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTTTTGCTGTTTGGATTTTTGCTATGGCCGCACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACTGTATTTTGTAATCGGCTGGAATAGCGCCGCATTATCCAAAGATTGATGTGT  >  CP006881/3528560‑3528834
                                                                                                                                         |                                                                                                                                         
aGTTTTGCTGTTTGGATTTTTGCTATGGCCGCACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGTAAAGCTCACAAAAg                                                                                                                                          <  3:298937/139‑1 (MQ=255)
      gCTGTTTGGATTTTTGCTATGGCCGCACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGAAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGcc                                                                                                                                     <  3:118302/138‑1 (MQ=255)
      gCTGTTTGGATTTTTGCTATGCCGGCACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATATTGCGGAAAGCTCACAAAAGCGGcc                                                                                                                                     <  5:367235/138‑1 (MQ=255)
      gCTGTTGGGATTTTTGCTATGGCCGCACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGcc                                                                                                                                     <  1:31750/138‑1 (MQ=255)
               aTTTTTGCTAGGGCCGCACTGATTGCATCATCTGCTGCCGGACGGTGTTTGGGCGCTGCAACAGCACCCAGGTTTTTCTTATTTGTGACTTCATACACAACATCTGGCGCAAACCTCAAAAACGCGGCCCCAGcctgcc                                                                                                                           <  4:211300/139‑1 (MQ=255)
               aTTTTGGATAGGGCCGCACTGATTGCATCATCGGCTGCAGCACCGCGTTTTGGCGCTGCAACCGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGTAAAGCTCACAAACGCGGCCCCAGcctgcc                                                                                                                           <  6:264499/139‑1 (MQ=255)
                    tGCTATGGCCGCACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCACCAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGcctgccctgat                                                                                                                      >  7:48220/1‑137 (MQ=255)
                    tGCTATGGCCGCACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGACAGCTCACAAAAGCGGCCCCAGCCTGCCctgct                                                                                                                      >  2:28860/1‑139 (MQ=255)
                    tGCTATGGCCGCACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAACGCGGCCCCAGCCTGCCctgct                                                                                                                      >  4:209379/1‑139 (MQ=255)
                     gatATGGCCGCACTGATTGCATCATTTGCTGCAGTACCGTTTTTTGGCGCTGAAACAGCACGCAGGTTTTTCGTTTTTGTGACTTCATTCACAACATCTTGCGCAAAGCTCAAAAAAGCGGCCCCAGCCTGCCctgct                                                                                                                      <  8:260307/136‑1 (MQ=255)
                        ccggCCGCACGGTTTGCATCATCTGCTGCCGGACCGAGTTTTGGCGCTGCAACAGCACGCAGGTTTTTCGTATTTGTGACTTCATTCACAAAAACTTGCGCAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACg                                                                                                                  <  7:42756/137‑1 (MQ=255)
                         tGGCCGCACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCATGCGGATAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGc                                                                                                                 >  6:354244/1‑139 (MQ=255)
                          ggCCGCCCTGATTGCATCAGCTGCTGCAGGACCGAGTTTGGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATACACAACATCTTGCGGAAAGCTCACAAACGCGGCCCCAGCCTGCCCTGCTGACGCt                                                                                                                <  6:65314/139‑1 (MQ=255)
                               cACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAACGCGGCCCCAGCCTGCCCTGCTGACGCTATcc                                                                                                            >  1:333835/1‑138 (MQ=255)
                                    aTTGCATCATCTGGTGCAGGACCTTGTTTGGGGGCGGCAACAGCACGCTCGTTTTGCGTATTTGGGACTTAATTCACAACATCTGCCGTAATCCTCACAAACGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTaaa                                                                                                        <  4:245550/137‑1 (MQ=255)
                                      tGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAAtctg                                                                                                    >  8:42756/1‑136 (MQ=255)
                                            atcTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGc                                                                                                                                >  8:171855/1‑105 (MQ=255)
                                            atcTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGc                                                                                                                                <  7:171855/105‑1 (MQ=255)
                                              ctgctgCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTaa                                                                                             >  7:321354/1‑138 (MQ=255)
                                                  tgcAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCt                                                                                        >  5:228194/1‑139 (MQ=255)
                                                  tgcAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCt                                                                                        >  3:38321/1‑139 (MQ=255)
                                                       gACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCgg                                                                                   >  4:173666/1‑139 (MQ=255)
                                                       gACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCgg                                                                                   >  2:299470/1‑139 (MQ=255)
                                                       gACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCgg                                                                                   >  3:123056/1‑139 (MQ=255)
                                                       gACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCgg                                                                                   >  2:85152/1‑139 (MQ=255)
                                                            aGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTatat                                                                              >  3:144706/1‑139 (MQ=255)
                                                            aGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTatat                                                                              >  6:122051/1‑139 (MQ=255)
                                                            aGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTatat                                                                              >  5:348813/1‑139 (MQ=255)
                                                                         cAACCGCACGCACGTTTAGCGTCTTTGGGACTACATCACCAACATCTTCCGCAACCCTCACAACCGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTg                                                                 <  6:25876/139‑1 (MQ=255)
                                                                         cAACAGCACGCACTTTTTTCTTTTTTGTGACTTCATTCAAAACTTCTTGCGTAAAGCTCACAAACGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTg                                                                 <  2:309469/139‑1 (MQ=255)
                                                                         cAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGTAAAGCTCACAAACGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTg                                                                 <  3:172689/139‑1 (MQ=255)
                                                                         cAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAACGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTg                                                                 <  8:321354/139‑1 (MQ=255)
                                                                         cAACAGCACGCACGTTTTTCGTATTTGTGACTTCATACACAACATCTGGCGCAACGCTCACAAACGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTg                                                                 <  5:95890/139‑1 (MQ=255)
                                                                              ccacgcacgTTTTTTTTTTTTTTGACTTCTTACACAACATGTTGCGGAACCCACAAAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACtt                                                            <  2:333835/138‑1 (MQ=255)
                                                                                 cgcacgTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTTAAGTTCTa                                                         >  4:208233/1‑139 (MQ=255)
                                                                                  gcaggTTTTTCGTATTTGTGATTAATTTCACAAAAACTTGCGTAACGCTCAAAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTac                                                        <  4:144706/139‑1 (MQ=255)
                                                                                   caggTTTTTCTTATTTGTTATTTCATCAAAAAAATATGGGGCAACGCTCACAAACGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTaca                                                       <  6:228194/136‑1 (MQ=255)
                                                                                   cacgTTTTTCTTATTTGTGACTTCATTCACAACATCTTGCGCAAAGCCCACAAACGCGGCCCCAGCCTGCCCTGCTGACGATATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTaca                                                       <  5:169084/139‑1 (MQ=255)
                                                                                   cacgTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTaca                                                       >  1:309469/1‑139 (MQ=255)
                                                                                   cacgTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTac                                                        >  3:343854/1‑138 (MQ=255)
                                                                                   cacgTTTTTCGTATTTGTCACTTCATTAACAACATCTTGCGCAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTaca                                                       <  4:123056/139‑1 (MQ=255)
                                                                                         tttCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACTGTAt                                                 >  7:288055/1‑139 (MQ=255)
                                                                                                     caCTTCATACCCAACATCTTGGGCAAAGCACCCAAACGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGAATATTTTTTACATCTTGAACTTCTACACTGTATTTTGTAATCGGc                                     <  7:318401/138‑1 (MQ=255)
                                                                                                                    aTCTTCCGGAAAGCTCACAAACGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACTGTATTTTGTAATCGGCTGGAATAGCGCCGCa                      <  8:186557/139‑1 (MQ=255)
                                                                                                                     acTTGCGCAACCCGCACAACCGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACTGTATTTTGTAATCGGCTGGAATAGCGCCGCAt                     <  2:4332/138‑1 (MQ=255)
                                                                                                                      cTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGGCGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACt                                                     <  7:244861/106‑1 (MQ=255)
                                                                                                                      cTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGGCGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACt                                                     >  8:244861/1‑106 (MQ=255)
                                                                                                                        tGCGGAAAGCTCACAAACGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCt                                                                   <  1:309695/90‑1 (MQ=255)
                                                                                                                        tGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCt                                                                   >  2:309695/1‑90 (MQ=255)
                                                                                                                         gCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACg                                                                                                                  <  4:230082/42‑1 (MQ=255)
                                                                                                                         gCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACg                                                                                                                  >  3:230082/1‑42 (MQ=255)
                                                                                                                          cGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACTGTATTTTGTAATCGGCTGGAATAGCGCCGCATTATcc                <  1:299470/139‑1 (MQ=255)
                                                                                                                          cGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACTGTATTTTGTAATCGGCTGGAATAGCGCCGCATTATcc                <  3:173666/139‑1 (MQ=255)
                                                                                                                               aGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTg                                                                 >  6:111222/1‑85 (MQ=255)
                                                                                                                               aGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTg                                                                 <  5:111222/85‑1 (MQ=255)
                                                                                                                               aGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACTGTATTTTGTATTCGGCTGGAATAGCGCCGCATTATCCa               >  4:305005/1‑135 (MQ=255)
                                                                                                                               aGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACTGTATTTTGTAATCGGCTGGAATAGCGCCGCATTATCCa               >  1:16013/1‑135 (MQ=255)
                                                                                                                                        aaGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACTTTATTTTGTAATCGGCTGGAATAGCGCCGCATTATCCAAAGATTGATgtgt  <  5:122051/139‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                         
AGTTTTGCTGTTTGGATTTTTGCTATGGCCGCACTGATTGCATCATCTGCTGCAGGACCGAGTTTTGGCGCTGCAACAGCACGCACGTTTTTCGTATTTGTGACTTCATTCACAACATCTTGCGGAAAGCTCACAAAAGCGGCCCCAGCCTGCCCTGCTGACGCTATCCTAAATGCATTTGTAACAGCTTCCGGTATATTTTTTACATCTTGAACTTCTACACTGTATTTTGTAATCGGCTGGAATAGCGCCGCATTATCCAAAGATTGATGTGT  >  CP006881/3528560‑3528834

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: ‑

GATK/CNVnator alignment

N/A