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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 385,798 C→T 30.0% G336G (GGC→GGT)  cstA → carbon starvation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE385,7980CT30.0% 149.7 / 78.7 110G336G (GGC→GGT) cstAcarbon starvation protein
Reads supporting (aligned to +/- strand):  ref base C (38/39);  new base T (20/13);  total (58/52)
Fisher's exact test for biased strand distribution p-value = 3.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 113 total aligned reads displayed.

TTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGG  >  minE/385728‑385864
                                                                      |                                                                  
ttGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGgc                                                                    >  1:5664158/1‑71 (MQ=255)
 tGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGgcg                                                                   >  1:454788/1‑71 (MQ=255)
     gATTGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgt                                                               <  1:5600569/71‑1 (MQ=255)
     gATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgt                                                               <  1:2073417/71‑1 (MQ=255)
       tGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgtgt                                                             <  1:381716/71‑1 (MQ=255)
       tGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgtg                                                              >  1:757379/1‑70 (MQ=255)
        ggCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTc                                                            >  1:3297794/1‑71 (MQ=255)
        ggCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTc                                                            >  1:1851656/1‑71 (MQ=255)
         gCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTc                                                            <  1:3043332/70‑1 (MQ=255)
         gCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCt                                                           <  1:2961331/71‑1 (MQ=255)
         gCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCt                                                           <  1:3771173/71‑1 (MQ=255)
         gCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCt                                                           <  1:208726/71‑1 (MQ=255)
         gCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCt                                                           >  1:1195516/1‑71 (MQ=255)
          cACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTg                                                          >  1:1514140/1‑71 (MQ=255)
           aCTGGCCCGGTGTGGTCGGGCAATGTGTTCCCCTTCCTGTTCATCACCATCGCCTGCGGCGCCgtc                                                              <  1:5583916/66‑2 (MQ=255)
           aCTGGCCCGGTGTGGTCGGGCAATGTGTTCCCCTTCCTGTTCATCACCATCGCCTGCGGCGCCgtc                                                              <  1:3076186/66‑2 (MQ=255)
            cTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGc                                                        >  1:3721522/1‑71 (MQ=255)
               gCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCC‑‑TGGCGCGGTGTCTGGCTTc                                                     <  1:2628831/69‑1 (MQ=255)
                     tATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTc                                                     <  1:4039023/65‑1 (MQ=255)
                       tGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgt                                                               <  1:5547667/53‑1 (MQ=255)
                       tGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGc                                                        <  1:5280871/60‑1 (MQ=255)
                         gACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTg                                            <  1:4515735/70‑1 (MQ=255)
                         gACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTg                                            <  1:1045122/70‑1 (MQ=255)
                          aCCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCAGTGGCGCGGTGTCTgg                                                         <  1:3608653/56‑1 (MQ=255)
                            cGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTc                                                            <  1:4457964/51‑1 (MQ=255)
                             ggTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAtctc                                       <  1:5356668/71‑1 (MQ=255)
                              gTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATctct                                      <  1:3691129/71‑1 (MQ=255)
                               tAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtctt                                     <  1:3370116/71‑1 (MQ=255)
                               tAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtctt                                     <  1:4003777/71‑1 (MQ=255)
                                aaCCTGTTCGCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtcttc                                    >  1:3309006/1‑71 (MQ=255)
                                aaCCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTg                                            >  1:1059454/1‑63 (MQ=255)
                                aaCCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtcttc                                    >  1:5359783/1‑71 (MQ=255)
                                  tcTGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGgt                                                               <  1:652291/41‑1 (MQ=38)
                                   cTGTTCCCGTTCCTGTTTTTCACCATCGCCTGTGGCGCGGTGTCTGGCTTc                                                     <  1:754599/51‑1 (MQ=255)
                                   cTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTc                                                     <  1:423090/51‑1 (MQ=255)
                                   cTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTc                                                     <  1:705027/51‑1 (MQ=255)
                                   cTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTc                                                     <  1:1546709/51‑1 (MQ=255)
                                   cTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTgg                                 <  1:4010256/71‑1 (MQ=255)
                                   cTGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGgt                                                               <  1:1652347/41‑1 (MQ=38)
                                   cTGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGAt                                          >  1:3604457/1‑62 (MQ=255)
                                   cTGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCgg                                 >  1:344535/1‑71 (MQ=255)
                                   cTGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCgg                                 >  1:3630361/1‑71 (MQ=255)
                                    tGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTgg                                 >  1:316871/1‑70 (MQ=255)
                                    tGTTCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCtcttccg                                  <  1:379824/69‑3 (MQ=255)
                                    tGTTCCCCTTCCTGTTCATCACCATCGCCTGCGGCGCCGTCTCGGGCTTcc                                                    >  1:3721054/1‑51 (MQ=19)
                                    tGTTCCCCTTCCTGTTCATCACCATCGCCTGCGGCGCCGTCTCGGGCTTCCa                                                   >  1:4937681/1‑52 (MQ=25)
                                    tGTTCCCCTTCCTGTTCATCACCATCGCCTGCGGCGCCGTCTCGGGCTTCCa                                                   >  1:179118/1‑52 (MQ=25)
                                     gTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCa                                                   >  1:3396405/1‑51 (MQ=255)
                                      ttCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCa                                                   >  1:1626343/1‑50 (MQ=255)
                                      ttCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCa                                                   >  1:2207877/1‑50 (MQ=255)
                                      ttCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTAc                              >  1:2880985/1‑71 (MQ=255)
                                       tcgcGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGAc                              >  1:2441857/4‑70 (MQ=255)
                                       tCCCGTTCCTGTTCATCACCATCGCCTGTGGtgcg                                                                 >  1:1075373/1‑35 (MQ=37)
                                        cccGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTc                                                     >  1:1554944/1‑46 (MQ=255)
                                        cccGTTCATGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTc                                                     >  1:1115606/1‑46 (MQ=255)
                                         ccGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCAc                           <  1:5355415/71‑1 (MQ=255)
                                           gTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGc                                                        >  1:2734362/1‑40 (MQ=37)
                                           gTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGc                         >  1:4703036/1‑71 (MQ=255)
                                           gTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGc                         >  1:201029/1‑71 (MQ=255)
                                           gTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGc                         >  1:5588902/1‑71 (MQ=255)
                                            ttCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGcc                        <  1:168692/71‑1 (MQ=255)
                                            ttCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGcc                        <  1:3677951/71‑1 (MQ=255)
                                             tCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCtcttc                                    >  1:2926318/1‑58 (MQ=255)
                                               cTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAt                                          >  1:1272292/1‑50 (MQ=255)
                                               cTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAt                                          >  1:577523/1‑50 (MQ=255)
                                               cTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAt                                          >  1:1213713/1‑50 (MQ=255)
                                               cTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAt                                          >  1:4105061/1‑50 (MQ=255)
                                               cTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGccaa                      <  1:345194/70‑3 (MQ=255)
                                                tGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtcttct                                   <  1:2502230/56‑1 (MQ=255)
                                                  tttATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                   <  1:1661703/70‑1 (MQ=255)
                                                  tttATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                   <  1:5116961/70‑1 (MQ=255)
                                                  tttATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                   <  1:1576820/70‑1 (MQ=255)
                                                        aCCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTgg             >  1:3700686/1‑70 (MQ=255)
                                                        aCCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGc            >  1:4549970/1‑71 (MQ=255)
                                                        aCCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGc            >  1:5469831/1‑71 (MQ=255)
                                                        aCCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGc            >  1:2658140/1‑71 (MQ=255)
                                                         ccATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTAcga                            <  1:1188041/54‑3 (MQ=255)
                                                         ccATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGct           <  1:3375521/71‑2 (MQ=255)
                                                            tCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaac        >  1:1952477/1‑71 (MQ=255)
                                                            tCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaac        >  1:5309445/1‑71 (MQ=255)
                                                             cGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaat        >  1:1707696/1‑69 (MQ=255)
                                                              gCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatg       >  1:5027682/1‑68 (MQ=255)
                                                              gCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatg       <  1:5170441/70‑3 (MQ=255)
                                                              gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg       <  1:133727/70‑1 (MQ=255)
                                                              gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg       <  1:4227084/70‑1 (MQ=255)
                                                              gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg       <  1:2238044/70‑1 (MQ=255)
                                                              gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg       <  1:2474919/70‑1 (MQ=255)
                                                              gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcgaacg       <  1:3113432/70‑1 (MQ=255)
                                                              gCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGcg           >  1:3418768/1‑66 (MQ=255)
                                                               ccTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatga      >  1:4632422/1‑70 (MQ=255)
                                                               ccTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatga      >  1:1528704/1‑70 (MQ=255)
                                                                cTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAg    >  1:2125439/1‑71 (MQ=255)
                                                                   tgGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGctaatgaaacc  <  1:89464/70‑4 (MQ=255)
                                                                   tgGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTACGACGCCAAAACTGCTGGct           <  1:1943278/61‑2 (MQ=255)
                                                                   tgGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                   >  1:2217885/1‑53 (MQ=255)
                                                                   tgGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                   >  1:3948685/1‑53 (MQ=255)
                                                                   tgGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGa                   >  1:2359027/1‑53 (MQ=255)
                                                                    ggCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATg                 >  1:4360710/1‑54 (MQ=255)
                                                                    ggCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATg                 >  1:2834309/1‑54 (MQ=255)
                                                                    ggCGCGGTGTCTGGCTTCCATGCGCTGATCTCTT‑AGGGACCACGCCGAAGATg                 >  1:2771463/1‑53 (MQ=255)
                                                                      |                                                                  
TTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAAGATGCTGGCGAACGAAGGG  >  minE/385728‑385864

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A