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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,919,429 C→T 10.4% S89S (TCG→TCA)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,4290CT10.4% 269.5 / 16.7 96S89S (TCG→TCA) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base C (48/37);  new base T (6/4);  total (55/41)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.41e-01

TCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATAT  >  minE/2919359‑2919495
                                                                      |                                                                  
tctcCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATc                                                                    >  1:2754572/1‑71 (MQ=255)
  tcCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGa                                                                  >  1:1711836/1‑71 (MQ=255)
  tcCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGa                                                                  >  1:3655131/1‑71 (MQ=255)
   ccTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGAc                                                                 >  1:1750873/1‑71 (MQ=255)
    cTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATc                                                                    <  1:2676158/67‑1 (MQ=255)
    cTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCg                                                                   <  1:3462241/68‑1 (MQ=255)
    cTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGAct                                                                >  1:2337930/1‑71 (MQ=255)
    cTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGAc                                                                 >  1:1923432/1‑70 (MQ=255)
       aCCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGActc                                                               <  1:342752/69‑1 (MQ=255)
       aCCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCtt                                                             >  1:1105342/1‑71 (MQ=255)
       aCCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCtt                                                             >  1:3646189/1‑71 (MQ=255)
        ccATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCttt                                                            <  1:1678526/71‑1 (MQ=255)
          aTAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTAt                                                          <  1:1988056/71‑1 (MQ=255)
           tAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTAt                                                          >  1:1231583/1‑70 (MQ=255)
           tAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTAt                                                          <  1:3021845/70‑1 (MQ=255)
           tAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATg                                                         <  1:1195531/71‑1 (MQ=255)
           tAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATg                                                         <  1:3527365/71‑1 (MQ=255)
           tAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTCTCTTTAATCGACTCTTTAt                                                          >  1:2264886/1‑70 (MQ=255)
              ccGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGa                                                        >  1:2516378/1‑69 (MQ=255)
              ccGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGAc                                                       >  1:287660/1‑70 (MQ=255)
              ccGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGAc                                                       >  1:3877993/1‑70 (MQ=255)
               cgcgATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGAcc                                                      >  1:3140073/1‑70 (MQ=255)
                 cgATACTGAATGCCGTCATACATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAAt                                                   >  1:3343308/1‑71 (MQ=255)
                 cgATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAAt                                                   <  1:1501430/71‑1 (MQ=255)
                 cgATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAAt                                                   <  1:1072865/71‑1 (MQ=255)
                   aTACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCt                                                 <  1:3140774/71‑1 (MQ=255)
                    tACTTAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCt                                                 <  1:3182861/70‑1 (MQ=255)
                    tACTGAATGCCGTCATACATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTg                                                >  1:1151001/1‑71 (MQ=255)
                        gAAAACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGAc                                                                 <  1:44526/50‑1 (MQ=255)
                         aaaaCCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTg                                            <  1:2421608/67‑1 (MQ=255)
                         aaTACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTgg                                               >  1:1196747/1‑67 (MQ=255)
                         aaTACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTg                                            <  1:3576235/70‑1 (MQ=255)
                         aaTACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTg                                            <  1:1588042/70‑1 (MQ=255)
                         aaTACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTg                                            <  1:3400262/70‑1 (MQ=255)
                          aTACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTAt                                                          >  1:3646598/1‑55 (MQ=255)
                           tACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATg                                                         <  1:1969164/55‑1 (MQ=255)
                           tACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCg                                         >  1:2875305/1‑71 (MQ=255)
                           tACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCg                                         <  1:1014431/71‑1 (MQ=255)
                             ccGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCt                                       <  1:530444/71‑1 (MQ=255)
                              cGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCtt                                      <  1:3216134/71‑1 (MQ=255)
                              cGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCtt                                      >  1:390611/1‑71 (MQ=255)
                                tCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTgg                                    <  1:3916074/71‑1 (MQ=255)
                                tCATACATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCgg                                    >  1:3047201/1‑71 (MQ=255)
                                   tACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                 <  1:3711769/71‑1 (MQ=255)
                                     cATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCtt                                                             <  1:1304227/41‑1 (MQ=255)
                                     cATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGcccta                               <  1:1101366/71‑3 (MQ=255)
                                      aTGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                 >  1:3325441/1‑68 (MQ=255)
                                      aTGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                 >  1:2753508/1‑68 (MQ=255)
                                        gCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTa                                                           >  1:64676/1‑40 (MQ=255)
                                        gCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCgaga                             >  1:286668/1‑70 (MQ=255)
                                        gCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCgaga                             >  1:1671216/1‑70 (MQ=255)
                                        gCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCgaga                             >  1:2474233/1‑70 (MQ=255)
                                         cGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGAt                            >  1:628717/1‑70 (MQ=255)
                                          gACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTAt                                                          <  1:3747826/39‑1 (MQ=255)
                                          gACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATaa                          <  1:1545066/71‑1 (MQ=255)
                                          gACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATaa                          <  1:3385590/71‑1 (MQ=255)
                                            ccAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGcc                                          <  1:1916688/53‑1 (MQ=255)
                                            ccAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAg                         >  1:1435759/1‑70 (MQ=255)
                                            ccAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAg                         >  1:3253438/1‑70 (MQ=255)
                                            ccAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAg                         >  1:2606645/1‑70 (MQ=255)
                                            ccAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAg                         >  1:3744153/1‑70 (MQ=255)
                                             cAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTa                       <  1:1338284/71‑1 (MQ=255)
                                             cAAGCACGCGGGCAGTGTCTTTAATAGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGt                        >  1:3808790/1‑70 (MQ=255)
                                               aGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAc                     <  1:800302/71‑1 (MQ=255)
                                               aGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAc                     >  1:2019871/1‑71 (MQ=255)
                                                 cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAcgc                   <  1:198903/71‑1 (MQ=255)
                                                 cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAcg                    >  1:1024561/1‑70 (MQ=255)
                                                   cgcgGGCAGTGTCTTTAATCGACTCTTTATGACCAATc                                                  <  1:3360299/38‑1 (MQ=255)
                                                   cgcgGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                 <  1:1212140/71‑1 (MQ=255)
                                                    gcgGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAg                >  1:3674753/1‑71 (MQ=255)
                                                    gcgGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAg                >  1:2676850/1‑71 (MQ=255)
                                                         cAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCAccc           >  1:1171111/1‑71 (MQ=255)
                                                          ggtgtCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCt                                       <  1:1502732/41‑1 (MQ=37)
                                                           gtgtCTTTAATCGACTCTTTATGACCAATCTGGCTGcc                                          >  1:80866/1‑38 (MQ=255)
                                                           gtgtCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGccc           <  1:1796656/69‑1 (MQ=255)
                                                            tgtCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTaa                      >  1:2262576/1‑57 (MQ=255)
                                                            tgtCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTgg        >  1:305225/1‑71 (MQ=255)
                                                            tgtCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTgg        >  1:3772954/1‑71 (MQ=255)
                                                            tgtCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAAc                     >  1:1536508/1‑58 (MQ=255)
                                                             gtCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTgg        <  1:1451349/70‑1 (MQ=255)
                                                             gtCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGt       >  1:2564401/1‑71 (MQ=255)
                                                             gtCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAAcgc                   <  1:1223077/59‑1 (MQ=255)
                                                              tCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCga                               >  1:1111400/1‑46 (MQ=255)
                                                              tCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                 >  1:135462/1‑60 (MQ=255)
                                                              tCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                 >  1:140120/1‑60 (MQ=255)
                                                              tCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                 >  1:3227485/1‑60 (MQ=255)
                                                                tttAATCGACTCTTTATGACCAATCTGGCTGCCGCt                                       <  1:1706149/36‑1 (MQ=255)
                                                                tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGt                        <  1:3029960/51‑1 (MQ=255)
                                                                tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAcgc                   <  1:2679631/56‑1 (MQ=255)
                                                                tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAg                >  1:456162/1‑59 (MQ=255)
                                                                tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa     >  1:3480390/1‑70 (MQ=255)
                                                                tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa     >  1:910340/1‑70 (MQ=255)
                                                                  tAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCaaat  >  1:3334071/1‑71 (MQ=255)
                                                                  tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCatat  >  1:1032572/1‑71 (MQ=255)
                                                                  tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAAGCGAGCACCCTGGTCatat  >  1:3624586/1‑71 (MQ=255)
                                                                   aaTTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCt          >  1:2810014/1‑62 (MQ=255)
                                                                    aTCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAc                     <  1:3024510/50‑1 (MQ=255)
                                                                     tCGACTCTTTATGACCAATCTGGCTGACGCTTGGGCCGAGATAAGTAACGCGAGCACCCt          >  1:1648351/1‑60 (MQ=255)
                                                                      |                                                                  
TCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATAT  >  minE/2919359‑2919495

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A