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 2,919,372 G→A 21.1% G108G (GGC→GGT)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,3720GA21.1% 276.2 / 61.8 137G108G (GGC→GGT) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base G (63/45);  new base A (18/11);  total (81/56)
Fisher's exact test for biased strand distribution p-value = 8.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 141 total aligned reads displayed.

CATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTAT  >  minE/2919302‑2919439
                                                                      |                                                                   
cATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAg                                                                     >  1:1217205/1‑71 (MQ=255)
     gTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCcgc                                                                 <  1:4780463/70‑1 (MQ=255)
     gTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCcgc                                                                 <  1:2973416/70‑1 (MQ=255)
     gTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCcgc                                                                 <  1:571441/70‑1 (MQ=255)
      tCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGa                                                               <  1:1858072/71‑1 (MQ=255)
        aGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGAt                                                              <  1:3962260/70‑1 (MQ=255)
        aGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATa                                                             >  1:2758018/1‑71 (MQ=255)
         ggCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGa                                                               <  1:241723/68‑1 (MQ=255)
         ggCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGa                                                               <  1:1413791/68‑1 (MQ=255)
          gCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACt                                                           <  1:1812446/71‑1 (MQ=255)
           ccgttCCACACCGGCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACt                                                           >  1:2042270/4‑70 (MQ=255)
           ccgttCCACACCGGCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACt                                                           >  1:306238/4‑70 (MQ=255)
           ccgttCCACACCGGCACGCCCGCATACTGCGCCAGCGGTTCGACCACTTCCTGGCCGTGACCGCGATACTg                                                          <  1:4983946/68‑1 (MQ=255)
           ccATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTg                                                          <  1:1675769/71‑1 (MQ=255)
            cgttCCACACCGTCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTg                                                          >  1:2836535/3‑70 (MQ=255)
            cATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGa                                                         <  1:4742506/71‑1 (MQ=255)
             gttCCACACCGGCACGCCCGCATACTGCGCCAGCGTATCGACCACTTCCTGGCCGTGACCGCGATACTg                                                          <  1:1508771/68‑1 (MQ=255)
              ttCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGa                                                               <  1:3283864/63‑1 (MQ=255)
               tCCACACCGGCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAAtg                                                      >  1:2279965/1‑70 (MQ=255)
                ccATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATAc                                                     >  1:402945/1‑71 (MQ=255)
                ccATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATAc                                                     >  1:2680694/1‑71 (MQ=255)
                ccATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATAc                                                     >  1:5014182/1‑71 (MQ=255)
                ccACACCGGCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAAtgc                                                     >  1:3211553/1‑69 (MQ=255)
                 cATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATa                                                      <  1:4792160/69‑1 (MQ=255)
                 cATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATAcc                                                    >  1:5485464/1‑71 (MQ=255)
                  aTACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCcgcg                                                                <  1:4121044/58‑1 (MQ=255)
                  aTACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCg                                                   <  1:1697541/71‑1 (MQ=255)
                  aTACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCg                                                   <  1:2367806/71‑1 (MQ=255)
                    aCCGGCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGt                                                  >  1:733439/1‑70 (MQ=255)
                     ccGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTc                                                 <  1:3940701/70‑1 (MQ=255)
                     ccGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCa                                                >  1:4518782/1‑71 (MQ=255)
                       ggCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                              <  1:2234140/71‑1 (MQ=255)
                       ggCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                              >  1:3176107/1‑71 (MQ=255)
                       ggCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                              >  1:4488857/1‑71 (MQ=255)
                        gCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATAc                                             <  1:3546077/71‑1 (MQ=255)
                        gCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                              >  1:484841/1‑70 (MQ=255)
                        gCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                              >  1:5183585/1‑70 (MQ=255)
                         cACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACa                                            >  1:10161/1‑71 (MQ=255)
                            gCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATa                                                             >  1:3112073/1‑51 (MQ=255)
                             cTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGc                                         >  1:78385/1‑70 (MQ=255)
                             cTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCg                                        <  1:5055038/71‑1 (MQ=255)
                             cTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCg                                        <  1:4496304/71‑1 (MQ=255)
                                  gTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGAcc                                     >  1:4983560/1‑69 (MQ=255)
                                  gTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGAcc                                     >  1:4695523/1‑69 (MQ=255)
                                   tATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCcgcg                                                                >  1:159110/1‑41 (MQ=255)
                                   tATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAg                                  >  1:4119429/1‑71 (MQ=255)
                                   tATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATAATGAATACCGTCATACATGCGACCAAg                                  >  1:5192670/1‑71 (MQ=255)
                                    aTTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAg                                  <  1:133222/70‑1 (MQ=255)
                                     ttCCGCCAGTGTTTCGACAATCTCCTGACCATAGcc                                                                   >  1:4921986/1‑36 (MQ=255)
                                     ttCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGaa                                                        >  1:1573367/1‑47 (MQ=255)
                                      tCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCa                                >  1:5674224/1‑70 (MQ=255)
                                       ccGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCAcg                              >  1:832260/1‑71 (MQ=255)
                                       ccGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCAc                               <  1:74845/70‑1 (MQ=255)
                                       ccGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCAc                               <  1:949554/70‑1 (MQ=255)
                                        cGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACa                                            >  1:975375/1‑56 (MQ=255)
                                        cGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCAcgc                             <  1:4914136/71‑1 (MQ=255)
                                        cGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTTAATGCCGTCATACATCCGCCCGAGAAc                               <  1:383035/69‑1 (MQ=255)
                                        cGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACATCCGCCCGAGAAc                               <  1:1889663/69‑1 (MQ=255)
                                         gCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGt                                                  <  1:305113/49‑1 (MQ=255)
                                           cAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCggg                          <  1:4073582/71‑1 (MQ=255)
                                             gtgtTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCggg                          >  1:1392164/1‑69 (MQ=255)
                                             gtgtTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCggg                          >  1:1101333/1‑69 (MQ=255)
                                             gtgtTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCggg                          >  1:3615736/1‑69 (MQ=255)
                                              cgtTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACATCCGCCCGAGAACCCgcgcgg                       >  1:1599345/2‑69 (MQ=255)
                                               gtTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACAtc                                          >  1:4166330/1‑50 (MQ=255)
                                               gtTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACAtc                                          >  1:1706309/1‑50 (MQ=255)
                                               gtTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACAtc                                          >  1:2186047/1‑50 (MQ=255)
                                                tttCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGa                                       <  1:4010447/53‑1 (MQ=255)
                                                tttCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGa                                       <  1:3460941/53‑1 (MQ=255)
                                                tttCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAgtg                     >  1:261763/1‑71 (MQ=255)
                                                tttCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAgt                      <  1:2736729/70‑1 (MQ=255)
                                                tttCGACAATCTCCTGACAATAGCCGCGATACTGAATACCGTCATAc                                             <  1:1045940/47‑1 (MQ=255)
                                                  tCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCa                                >  1:137224/1‑58 (MQ=255)
                                                  tCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTc                   >  1:4688723/1‑71 (MQ=255)
                                                  tCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTc                   >  1:161096/1‑71 (MQ=255)
                                                   cGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCa                                >  1:3830768/1‑57 (MQ=255)
                                                    gACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCtt                 <  1:5474177/71‑1 (MQ=255)
                                                    gACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCtt                 <  1:2301822/71‑1 (MQ=255)
                                                      cAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCa                                >  1:5171538/1‑54 (MQ=255)
                                                       aaTCTCCTGACCATAGCCGCGGTACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTaa              >  1:1903331/1‑71 (MQ=255)
                                                       aaTCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCAcgc                             >  1:2663031/1‑56 (MQ=255)
                                                             cTGACCATAGCCGCTATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGAct        >  1:4619687/1‑71 (MQ=255)
                                                             cTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATc            <  1:1424075/67‑1 (MQ=255)
                                                             cTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATc            >  1:1537469/1‑67 (MQ=255)
                                                             cTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGa          >  1:2821532/1‑69 (MQ=255)
                                                             cTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGa          >  1:5649331/1‑69 (MQ=255)
                                                             cTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGAct        >  1:2343272/1‑71 (MQ=255)
                                                             cTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGAGTCTTTAATCGAct        >  1:772278/1‑71 (MQ=255)
                                                              tGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGActc       >  1:5559379/1‑71 (MQ=255)
                                                                aCCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCa                                >  1:1658580/1‑44 (MQ=255)
                                                                aCCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCa                                >  1:4250198/1‑44 (MQ=255)
                                                                aCCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAgtgt                    >  1:2735544/1‑56 (MQ=255)
                                                                 ccATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGa          >  1:2899789/1‑65 (MQ=255)
                                                                  cATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCttt    >  1:242901/1‑70 (MQ=255)
                                                                   aTAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTAt  >  1:612447/1‑71 (MQ=255)
                                                                    tAGCCGCGATACTGAATACCGTCATACATGCGACCAAg                                  <  1:3016552/38‑1 (MQ=255)
                                                                    tAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTAt  >  1:3135233/1‑70 (MQ=255)
                                                                      gCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATc            >  1:4397023/1‑58 (MQ=255)
                                                                      gCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGa          >  1:2471840/1‑60 (MQ=255)
                                                                      gCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGa          >  1:1259896/1‑60 (MQ=255)
                                                                      |                                                                   
CATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTAT  >  minE/2919302‑2919439

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