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
A2 F999 I1 R1 226 132.7 9745491 85.7% 8351885 75.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,255,616 Δ1 bp intergenic (‑19/+312) yhaO ← / ← yhaP putative transport system permease protein/putative L‑serine dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,255,6150G.98.9% 396.3 / ‑4.4 88intergenic (‑18/+313)yhaO/yhaPputative transport system permease protein/putative L‑serine dehydratase
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base . (33/54);  total (33/55)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGGCACGACCCGCCGGGGTCGAAGGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCTTATTATTT  >  NC_000913/3255539‑3255689
                                                                            |                                                                          
gtgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAg                                                                            >  2:659928/1‑76 (MQ=255)
gtgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAg                                                                            <  2:1685709/76‑1 (MQ=255)
 tgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCGCGACCCGCCGGGGTCGAAgc                                                                           <  1:2096421/76‑2 (MQ=255)
 tgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAgc                                                                           >  2:1100482/1‑75 (MQ=255)
 tgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAgc                                                                           <  1:2662318/76‑2 (MQ=255)
 tgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAgc                                                                           >  2:838871/1‑75 (MQ=255)
  gtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAgcg                                                                          >  1:3554991/1‑74 (MQ=255)
   tCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAgcgt                                                                         >  2:1808816/1‑73 (MQ=255)
      gTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTg                                                                     <  2:3808556/76‑1 (MQ=255)
       tACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGc                                                                    <  1:3396071/76‑1 (MQ=255)
       gaCTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGc                                                                    <  2:4811565/75‑1 (MQ=255)
         cTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCaa                                                                  <  1:4216706/76‑1 (MQ=255)
          tGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAAt                                                                 <  2:532260/76‑1 (MQ=255)
           gTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATg                                                                >  2:3323808/1‑76 (MQ=255)
           gTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATg                                                                >  1:4141840/1‑76 (MQ=255)
            tCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGa                                                               <  1:3322363/76‑1 (MQ=255)
            tCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGa                                                               <  2:2604237/76‑1 (MQ=255)
            tCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGa                                                               >  1:1296636/1‑76 (MQ=255)
             cGAATTTGATCGCTTCTCCCCCCTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGAc                                                              <  2:1708721/76‑1 (MQ=255)
              gAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACg                                                             >  1:2761848/1‑76 (MQ=255)
              gAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACg                                                             <  1:1501459/76‑1 (MQ=255)
              gAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACg                                                             >  2:3646173/1‑76 (MQ=255)
                 tttGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCt                                                          <  1:2098615/76‑1 (MQ=255)
                  ttGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCtt                                                         <  2:3362871/76‑1 (MQ=255)
                  tggATCGCTGCTCGCCACTCGCTCGCACTCATTCCA‑GCACGACCCGCCTGGGTCGAA‑GCGTCTGCAATGACGCCtt                                                         <  1:3364600/74‑1 (MQ=255)
                   tGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCttt                                                        <  1:4587099/76‑1 (MQ=255)
                     gtCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTaa                                                      <  2:3264854/75‑2 (MQ=255)
                      tCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTAtt                                                     <  2:4243153/76‑1 (MQ=255)
                       cGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTc                                                    >  2:4663674/1‑76 (MQ=255)
                        gCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCg                                                   >  2:3060237/1‑76 (MQ=255)
                        gCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCg                                                   <  1:2699187/76‑1 (MQ=255)
                        gCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCg                                                   >  1:637403/1‑76 (MQ=255)
                         cTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGa                                                  >  2:3475519/1‑76 (MQ=255)
                          ttCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGAt                                                 >  1:121141/1‑76 (MQ=255)
                          ttCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGAt                                                 <  1:1898908/76‑1 (MQ=255)
                          ttCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGAt                                                 <  1:2048822/76‑1 (MQ=255)
                           tctcGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCgctc                                                >  2:27170/1‑73 (MQ=255)
                           tctcGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATg                                                <  2:4185032/76‑1 (MQ=255)
                            ctcGCCACTCGCACTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGc                                               <  2:3470688/76‑1 (MQ=255)
                             tcGCGACGCGCTCTCACTCATTCCA‑GCACGTCCCGCCGGGGTCGAA‑GCGGCTGCAATGACGCGTGTATGCGATGCa                                              >  1:2687634/1‑76 (MQ=255)
                              cGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCaa                                             <  2:3139512/76‑1 (MQ=255)
                               gCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAAt                                            >  2:2168457/1‑76 (MQ=255)
                               cccACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAAt                                            <  1:2428144/75‑1 (MQ=255)
                                 cACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAAttt                                          <  1:4396761/76‑1 (MQ=255)
                                 cACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAAttt                                          <  1:892571/76‑1 (MQ=255)
                                 cACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAAttt                                          <  2:1744955/76‑1 (MQ=255)
                                  ccTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTc                                         <  1:690187/75‑1 (MQ=255)
                                  aCTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTc                                         >  2:1382972/1‑76 (MQ=255)
                                   cTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTcc                                        <  1:200002/76‑1 (MQ=255)
                                   cTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTcc                                        >  2:3222541/1‑76 (MQ=255)
                                    tCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCa                                       >  2:798592/1‑76 (MQ=255)
                                    tCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCa                                       >  2:3354575/1‑76 (MQ=255)
                                     cGCTCTCACACATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCAt                                      <  1:1229584/76‑1 (MQ=255)
                                     cGCTCTAACTCATTCCA‑GCACGCCCCGCCGGAGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCAt                                      <  1:2834731/76‑1 (MQ=255)
                                      gCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATa                                     <  1:1808817/76‑1 (MQ=255)
                                      gCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATa                                     >  2:4858759/1‑76 (MQ=255)
                                       ctctCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATaa                                    >  2:4065187/1‑76 (MQ=255)
                                           cactcaTTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATACTTtc                                >  2:4748983/1‑76 (MQ=255)
                                             ctcaTTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTtctc                              <  2:4696416/76‑1 (MQ=255)
                                                 ttCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTc                          <  2:2434982/76‑1 (MQ=255)
                                                 ttCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTc                          <  2:2462677/76‑1 (MQ=255)
                                                 ttCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTc                          <  2:2497022/76‑1 (MQ=255)
                                                 ttCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTc                          <  1:3542385/76‑1 (MQ=255)
                                                      agCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCCata                      >  2:545905/2‑76 (MQ=255)
                                                      agCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAata                      >  2:509232/2‑76 (MQ=255)
                                                      agCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAata                      <  1:562979/75‑1 (MQ=255)
                                                       gCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAatat                     <  2:2097211/76‑1 (MQ=255)
                                                       gCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAatat                     >  2:3974430/1‑76 (MQ=255)
                                                       gCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAatat                     <  1:1952638/76‑1 (MQ=255)
                                                        cACGCCCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATAtt                    <  1:1907063/76‑1 (MQ=255)
                                                         aCGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATAttt                   >  1:4792584/1‑76 (MQ=255)
                                                         aCGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATAttt                   <  1:1948841/76‑1 (MQ=255)
                                                            gcccGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTGTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGt                <  2:812791/75‑1 (MQ=255)
                                                            aCCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGt                >  2:1750190/1‑76 (MQ=255)
                                                            aCCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGt                <  2:232963/76‑1 (MQ=255)
                                                              ccgccgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAg              >  1:2217948/1‑76 (MQ=255)
                                                              ccgccgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAg              <  2:1974680/76‑1 (MQ=255)
                                                               cgccgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAgg             <  1:1357091/76‑1 (MQ=255)
                                                                gccgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAggg            >  1:489933/1‑76 (MQ=255)
                                                                gccgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAggg            <  2:2054195/76‑1 (MQ=255)
                                                                gccgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAggg            >  1:4034670/1‑76 (MQ=255)
                                                                gccgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAggg            <  1:3974430/76‑1 (MQ=255)
                                                                gccgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAggg            <  1:287345/76‑1 (MQ=255)
                                                                 ccgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGc           <  2:4038108/76‑1 (MQ=255)
                                                                 ccgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGc           <  2:1872273/76‑1 (MQ=255)
                                                                  cgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCt          >  2:462121/1‑76 (MQ=255)
                                                                  cgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCt          <  2:2904497/76‑1 (MQ=255)
                                                                  cgGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCt          <  2:2885404/76‑1 (MQ=255)
                                                                   ggggTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCtt         <  2:1893865/76‑1 (MQ=255)
                                                                    gggTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAata                      >  2:473862/1‑62 (MQ=255)
                                                                    gggTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAata                      <  1:473862/62‑1 (MQ=255)
                                                                     ggTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCttat       >  1:542044/1‑76 (MQ=255)
                                                                      gTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCttatt      <  1:3305808/76‑1 (MQ=255)
                                                                      gTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCttatt      >  1:1626507/1‑76 (MQ=255)
                                                                       tCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGCCttatta     >  2:2971623/1‑76 (MQ=255)
                                                                           aGGCGTCTGAAATGATGCCTTTATGCGATGCAGTTTCCAGACTGTCTCGCGCATGATTGTGTAGGGCTtattatgt  <  2:4477155/76‑3 (MQ=255)
                                                                            |                                                                          
GTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGGCACGACCCGCCGGGGTCGAAGGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCTTATTATTT  >  NC_000913/3255539‑3255689

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A