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
A1 F28 I1 R1 163 52.9 1786516 99.3% 1774010 139.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,203,305 T→C R460R (CGT→CGC)  zraS → sensory histidine kinase ZraS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,203,3050TC96.7% 198.0 / ‑2.4 60R460R (CGT→CGC) zraSsensory histidine kinase ZraS
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base C (28/30);  total (29/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TAAAGCCGAAGGCACCGGATTGGGGCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGTAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAACGTCGCGCTGGCGAACAGCGGGCGACAGGC  >  NC_000913/4203170‑4203441
                                                                                                                                       |                                                                                                                                        
tAAAGCCGAAGGCACCGGATTGGGGCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAgg                                                                                                                                      <  1:120707/140‑1 (MQ=255)
 aaaGCCGAAGGCACCGGATTGGGGCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGa                                                                                                                                     <  1:258023/140‑1 (MQ=255)
  aaGCCGAAGGCACCGGATTGGGGCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGAc                                                                                                                                    >  1:90038/1‑140 (MQ=255)
       gAAGGCACCGGATTGGGGCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCcaca                                                                                                                               <  1:675969/140‑1 (MQ=255)
               cGGATTGGGGCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGAc                                                                                                                       >  1:419674/1‑140 (MQ=255)
                ggATTGGGGCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACg                                                                                                                      <  1:88961/140‑1 (MQ=255)
                ggATTGGGGCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACg                                                                                                                      <  2:781551/140‑1 (MQ=255)
                      gggCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGat                                                                                                                <  2:90038/140‑1 (MQ=255)
                      gggCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGat                                                                                                                >  1:542172/1‑140 (MQ=255)
                        gCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGataa                                                                                                              <  1:633744/140‑1 (MQ=255)
                         cTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGataat                                                                                                             >  2:81705/1‑140 (MQ=255)
                            gCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATc                                                                                                          >  1:468100/1‑140 (MQ=255)
                            gCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATc                                                                                                          >  2:678513/1‑140 (MQ=255)
                            gCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATc                                                                                                          >  1:616453/1‑140 (MQ=255)
                                tCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGata                                                                                                      >  1:460570/1‑140 (MQ=255)
                                        aataTTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCtggtg                                                                                              <  2:419674/140‑1 (MQ=255)
                                         atatTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCtggtgg                                                                                             <  2:206591/140‑1 (MQ=255)
                                          tatTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGTAAGGACCCACAAGGATGACGCACGATAATATCGATATTCtggtggt                                                                                            >  2:327481/1‑140 (MQ=255)
                                                  aacaacACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGatgatg                                                                                    >  1:46957/1‑140 (MQ=255)
                                                    caacaCGGTAGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGAc                                                                                  >  1:631860/1‑140 (MQ=255)
                                                       cacGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGGAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACAtt                                                                               <  2:616453/140‑1 (MQ=255)
                                                       cacGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACAtt                                                                               <  2:407369/140‑1 (MQ=255)
                                                         cGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAg                                                                             >  1:458605/1‑140 (MQ=255)
                                                          ggtggtACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGc                                                                            <  2:471744/140‑1 (MQ=255)
                                                            tggtACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCa                                                                          >  1:160586/1‑140 (MQ=255)
                                                               tACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTg                                                                       <  2:619089/140‑1 (MQ=255)
                                                                 cAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCa                                                                     >  1:842752/1‑140 (MQ=255)
                                                                      cAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCa                                                                     <  1:340722/135‑1 (MQ=255)
                                                                      cAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCa                                                                     >  2:340722/1‑135 (MQ=255)
                                                                      cAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTAtt                                                                >  2:126947/1‑140 (MQ=255)
                                                                      cAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTAtt                                                                >  2:639953/1‑140 (MQ=255)
                                                                      cAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTAtt                                                                >  2:185444/1‑140 (MQ=255)
                                                                        ggTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGTAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTAtttt                                                              <  1:327481/140‑1 (MQ=255)
                                                                        ggTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTAtttt                                                              >  1:624878/1‑140 (MQ=255)
                                                                        ggTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTAtttt                                                              <  2:624878/140‑1 (MQ=255)
                                                                        ggTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTAtttt                                                              <  2:468100/140‑1 (MQ=255)
                                                                         gTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTAtttgg                                                             >  2:825893/1‑138 (MQ=255)
                                                                         gTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTg                                                             <  1:467227/140‑1 (MQ=255)
                                                                          tCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGc                                                            <  2:46957/140‑1 (MQ=255)
                                                                          tCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGc                                                            <  2:831977/140‑1 (MQ=255)
                                                                          tCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGc                                                            <  2:631860/140‑1 (MQ=255)
                                                                          tCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGc                                                            <  2:460570/140‑1 (MQ=255)
                                                                          tCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGc                                                            <  1:806060/140‑1 (MQ=255)
                                                                             cAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCTCTATTTTGCAgg                                                         <  1:81705/140‑1 (MQ=255)
                                                                                       gggAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTgcg                                               <  1:684906/140‑1 (MQ=255)
                                                                                       gggAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTgcg                                               <  2:178164/140‑1 (MQ=255)
                                                                                         gAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGcgcg                                             <  2:687840/140‑1 (MQ=255)
                                                                                          aaaaGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCgg                                            >  1:419246/1‑140 (MQ=255)
                                                                                           aaaGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGc                                           <  2:663084/140‑1 (MQ=255)
                                                                                              ggCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTgg                                        <  2:419246/140‑1 (MQ=255)
                                                                                               gCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTggg                                       >  1:528157/1‑140 (MQ=255)
                                                                                                cTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTgggg                                      >  2:68266/1‑140 (MQ=255)
                                                                                                       ttCACCCTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAAc                               >  1:484684/1‑140 (MQ=255)
                                                                                                           cccTCTGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAACGTcg                           >  2:823650/1‑140 (MQ=255)
                                                                                                               ctGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAACGTCGCGCt                       >  2:185258/1‑140 (MQ=255)
                                                                                                                tGGCTTCCGGTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAACGTCGCGCTg                      >  1:214725/1‑140 (MQ=255)
                                                                                                                        ggTCAATATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAACGTCGCGCTGGCGAACAg              <  2:160586/140‑1 (MQ=255)
                                                                                                                            aaTATTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAACGTCGCGCTGGCGAACAGCggg          >  2:40099/1‑140 (MQ=255)
                                                                                                                               atTACGCGCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAACGTCGCGCTGGCGAACAGCGGGCGa       <  2:808859/140‑1 (MQ=255)
                                                                                                                                   cgcgCAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAACGTCGCGCTGGCGAACAGCGGGCGACAgg   >  1:75246/1‑140 (MQ=255)
                                                                                                                                    gcgcAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAACGTCGCGCTGGCGAACAGCGGGCGACAGGc  <  1:40099/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                        
TAAAGCCGAAGGCACCGGATTGGGGCTGGCGGTCGTGCATAATATTGTTGAACAACACGGTGGTACAATTCAGGTCGCAAGCCAGGAGGGAAAAGGCTCAACGTTCACCCTCTGGCTTCCGGTCAATATTACGCGTAAGGACCCACAAGGATGACGCACGATAATATCGATATTCTGGTGGTGGATGATGACATTAGCCACTGCACTATTTTGCAGGCTTTACTGCGCGGCTGGGGCTATAACGTCGCGCTGGCGAACAGCGGGCGACAGGC  >  NC_000913/4203170‑4203441

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A