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 2,919,240 T→C 27.6% K152K (AAA→AAG)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,2400TC27.6% 169.5 / 78.4 116K152K (AAA→AAG) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base T (42/42);  new base C (17/15);  total (59/57)
Fisher's exact test for biased strand distribution p-value = 8.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

Only 100 of 125 total aligned reads displayed.

CTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCATTGGT  >  minE/2919170‑2919308
                                                                      |                                                                    
cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                                      <  1:3143561/71‑1 (MQ=255)
cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                                      <  1:4436257/71‑1 (MQ=255)
cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                                      <  1:5233290/71‑1 (MQ=255)
cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                                      <  1:3830421/71‑1 (MQ=255)
   ccaGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTg                                                                   >  1:3993969/3‑71 (MQ=255)
   cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTg                                                                   >  1:659017/1‑71 (MQ=255)
   cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTg                                                                   >  1:3881427/1‑71 (MQ=255)
    gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGc                                                                  >  1:2560428/1‑71 (MQ=255)
    gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGc                                                                  >  1:4409404/1‑71 (MQ=255)
    gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACAAGCGTCATTTCGTTGAACGATTTGc                                                                  >  1:2598751/1‑71 (MQ=255)
    caGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTga                                                                  >  1:3453267/2‑70 (MQ=255)
     aGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGc                                                                  <  1:3308479/70‑1 (MQ=255)
        aTCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                                                              <  1:5507909/71‑1 (MQ=255)
        aTCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                                                              <  1:4243788/71‑1 (MQ=255)
         tCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                                                              >  1:5584906/1‑70 (MQ=255)
         tCGAATTGCCCGTGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCggg                                                              >  1:4874228/1‑70 (MQ=255)
         tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                                    <  1:1921360/64‑1 (MQ=255)
         tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                                    <  1:921967/64‑1 (MQ=255)
         tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                                    <  1:949611/64‑1 (MQ=255)
           gagttGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                                                              >  1:2192853/4‑68 (MQ=255)
           gagttGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                                                              >  1:1837444/4‑68 (MQ=255)
           gagttGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                                                              >  1:4565363/4‑68 (MQ=255)
           gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                                                            <  1:4625081/70‑1 (MQ=255)
             aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAAt                                                         >  1:3432057/1‑71 (MQ=255)
             aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAAt                                                         >  1:1202170/1‑71 (MQ=255)
               tGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGc                                                       >  1:663767/1‑71 (MQ=255)
                gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGc                                                       <  1:3308099/70‑1 (MQ=255)
                gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGc                                                       <  1:3273038/70‑1 (MQ=255)
                gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGc                                                       <  1:181489/70‑1 (MQ=255)
                gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCt                                                      >  1:5246231/1‑71 (MQ=255)
                 cccATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                                                     <  1:5137429/71‑1 (MQ=255)
                    aTGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCgg                                                               <  1:760622/58‑1 (MQ=255)
                     tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc                                                                 <  1:2221004/55‑1 (MQ=255)
                     tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                                                     <  1:5407096/67‑1 (MQ=255)
                     tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                                                     <  1:4580676/67‑1 (MQ=255)
                     tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTg                                                  >  1:4613013/1‑70 (MQ=255)
                     tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGc                                                 <  1:2808378/71‑1 (MQ=255)
                       ttgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaaa                                                          >  1:3554266/1‑60 (MQ=255)
                       ttgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                                                            <  1:4470762/58‑1 (MQ=255)
                       ttgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                                                     >  1:1514884/1‑65 (MQ=255)
                       ttgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                                                     >  1:4593094/1‑65 (MQ=255)
                        tgttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATg                                              >  1:911300/1‑71 (MQ=255)
                        tgttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATg                                              >  1:3016110/1‑71 (MQ=255)
                        tgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCgg                                                               <  1:373920/54‑1 (MQ=255)
                        tgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCgg                                                               >  1:2894917/1‑54 (MQ=255)
                         gttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCt                                                      >  1:647392/1‑62 (MQ=255)
                          ttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATTGt                                            <  1:2013748/71‑1 (MQ=255)
                           tACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATg                                              >  1:2044921/1‑68 (MQ=255)
                           tACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATg                                              >  1:4202588/1‑68 (MQ=255)
                              gcgcgTCACGTGCATAGACCAGCGTCATTTCGTTGTACGCt                                                                      <  1:3950997/41‑1 (MQ=38)
                                    cACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTg                                                  <  1:3114670/55‑1 (MQ=255)
                                    cACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATcc                                  >  1:2351368/1‑71 (MQ=255)
                                     aCCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCg                                 >  1:1206329/1‑71 (MQ=255)
                                         gCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGcc                               <  1:5354942/69‑1 (MQ=255)
                                         gCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGcc                               <  1:5039536/69‑1 (MQ=255)
                                          cATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCt                                                      <  1:3144619/45‑1 (MQ=255)
                                          cATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCt                                                      <  1:4560080/45‑1 (MQ=255)
                                           gtAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCcagca                           <  1:3256820/70‑1 (MQ=255)
                                           aTAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcagca                           <  1:2980714/71‑1 (MQ=255)
                                            tAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcagcag                          <  1:200232/71‑1 (MQ=255)
                                              gACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCa                                                >  1:914893/1‑47 (MQ=255)
                                              gACCAGCGCCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCt                        >  1:5551481/1‑71 (MQ=255)
                                               aCCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTg                       >  1:4465203/1‑71 (MQ=255)
                                               aCCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTg                       <  1:3663917/71‑1 (MQ=255)
                                               aCCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTTCATGGTCATCAGGTCCGCCAGCAGCt                        <  1:79489/70‑1 (MQ=255)
                                                ccAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcagcag                          >  1:3137687/1‑67 (MQ=255)
                                                ccAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGc                      <  1:3548393/71‑1 (MQ=255)
                                                 cAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCt                        >  1:3230000/1‑68 (MQ=255)
                                                 cAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGc                      <  1:2206133/70‑1 (MQ=255)
                                                 cAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCg                     <  1:2776115/71‑1 (MQ=255)
                                                 cAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTACTGCATGGTGAGAAGATCCGCcagcag                          >  1:5283254/1‑66 (MQ=255)
                                                   gCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGtc                   <  1:3738147/71‑2 (MQ=255)
                                                    cGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGtc                   <  1:1594569/70‑2 (MQ=255)
                                                     gTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGt                                            >  1:3611139/1‑44 (MQ=16)
                                                      tCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTcggg                <  1:988855/71‑2 (MQ=255)
                                                      tCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTcggg                >  1:958237/1‑70 (MQ=255)
                                                        aTTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGAt                                    >  1:4524402/1‑49 (MQ=255)
                                                        aTTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGAt                                    >  1:5114721/1‑49 (MQ=255)
                                                        aTTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGAt               >  1:2937142/1‑70 (MQ=255)
                                                        aTTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGAt               >  1:1165251/1‑70 (MQ=255)
                                                         tttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATg              >  1:1521858/1‑70 (MQ=255)
                                                          ttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg             >  1:4612318/1‑70 (MQ=255)
                                                          ttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg             <  1:98710/70‑1 (MQ=255)
                                                          ttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg             >  1:2694170/1‑70 (MQ=255)
                                                           tCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTcggg                >  1:1377731/1‑65 (MQ=255)
                                                           tCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTcggg                >  1:203654/1‑65 (MQ=255)
                                                           tCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTCGGGTGGaa           >  1:4193708/1‑71 (MQ=255)
                                                             gTTGTACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACt         <  1:5298801/71‑1 (MQ=255)
                                                             gTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACt         <  1:2503699/71‑1 (MQ=255)
                                                              ttGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACt         <  1:4187329/70‑1 (MQ=255)
                                                               tGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcagc                            <  1:2175456/50‑1 (MQ=255)
                                                               tGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg             <  1:5487741/65‑1 (MQ=255)
                                                               tGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTcg       >  1:3286920/1‑70 (MQ=255)
                                                                gAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCAt      >  1:641879/1‑71 (MQ=255)
                                                                gAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCAt      >  1:3541285/1‑71 (MQ=255)
                                                                aaaCGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTCGGGTgg             <  1:2672590/63‑1 (MQ=255)
                                                                aaaCGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTCGGGTGGAACTcg       <  1:1719064/69‑2 (MQ=255)
                                                                 aaCGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTCGGGTGGAACTcgt      <  1:893408/70‑3 (MQ=255)
                                                                   cGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCATTgg   >  1:1824122/1‑71 (MQ=255)
                                                                    gCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCATTGGt  <  1:3591007/71‑1 (MQ=255)
                                                                      |                                                                    
CTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCATTGGT  >  minE/2919170‑2919308

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