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 2,919,000 A→G 13.6% D232D (GAT→GAC)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,0000AG13.6% 221.0 / 23.4 88D232D (GAT→GAC) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base A (43/33);  new base G (6/6);  total (49/39)
Fisher's exact test for biased strand distribution p-value = 7.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

Only 100 of 105 total aligned reads displayed.

CCTGATATTCACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCCCACCAT  >  minE/2918930‑2919070
                                                                      |                                                                      
 cTGATATTCACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACAt                                                                       >  1:1749662/1‑71 (MQ=255)
   gATATTCACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCg                                                                     >  1:1249276/1‑71 (MQ=255)
    atatTCACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATc                                                                      <  1:1851072/69‑1 (MQ=255)
    atatTCACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATc                                                                      <  1:355764/69‑1 (MQ=255)
     tatTCACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCgg                                                                    <  1:50180/70‑1 (MQ=255)
       ttCACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGta                                                                  <  1:1807509/70‑1 (MQ=255)
       ttCACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGta                                                                  <  1:1984513/70‑1 (MQ=255)
        ccgcGCAGCAGCGCAATCCGCTCTGCCCACTTCTCTTTGGCCTCGCCCATCGACACCCACACGTCGGtata                                                                <  1:1419790/68‑1 (MQ=255)
         cACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGta                                                                  >  1:3654838/1‑68 (MQ=255)
         cACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGta                                                                  >  1:2973078/1‑68 (MQ=255)
           cGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGCCACCCACACATCGGTATAGa                                                              >  1:2953382/1‑70 (MQ=255)
            gcagcaGCGCAATCCGCTCTGCCCACTTCTCTTTGGCCTCGCCCATCGACACCCACACGTCGGTATAGAt                                                             >  1:651492/1‑70 (MQ=255)
               gcaatgcaatCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAg                                                         <  1:819556/71‑1 (MQ=255)
                caatgcaatCCGTTCCGCCAATTTCTCTTTTGCTTCCCCCATCGACACCcacaca                                                                        >  1:1198134/1‑55 (MQ=255)
                 aatgcaatCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGt                                                        <  1:3871636/70‑1 (MQ=255)
                 aatgcaatCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGt                                                        >  1:302257/1‑70 (MQ=255)
                   tgcaatCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGt                                                        <  1:1206775/68‑1 (MQ=255)
                   tgcaatCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTc                                                       >  1:1119927/1‑69 (MQ=255)
                     caatCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCgg                                                                    >  1:3543184/1‑54 (MQ=255)
                     caatCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCgg                                                                    >  1:1299522/1‑54 (MQ=255)
                     caatCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCa                                                   >  1:893447/1‑71 (MQ=255)
                       atCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCAc                                                  >  1:2022788/1‑70 (MQ=255)
                        tCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCg                                                                     >  1:71625/1‑50 (MQ=255)
                        tCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCAcc                                                 >  1:1399315/1‑70 (MQ=255)
                        tCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCAcc                                                 >  1:3408915/1‑70 (MQ=255)
                        tCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCt                                                <  1:1084522/71‑1 (MQ=255)
                        tCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCt                                                <  1:3320291/71‑1 (MQ=255)
                        tCCGCTCTGCCCACTTCTCTTTGGCCTCGCCCATCGACACCCACACGTCGGTATAGATAAAGTCCGCGccc                                                >  1:2377632/1‑70 (MQ=255)
                        tCCGCTCTGCCCACTTCTCTCTGGCCTCGCCCATCGACACCCACACGTCGGTATAGATAAAGTCCGCGccc                                                >  1:2449673/1‑70 (MQ=255)
                          cGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTc                                              <  1:657793/71‑1 (MQ=255)
                          cGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTc                                              <  1:1222338/71‑1 (MQ=255)
                              ccGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACt                                          >  1:3360828/1‑71 (MQ=255)
                              ccGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACt                                          >  1:3549542/1‑71 (MQ=255)
                               tgCCCACTTCTCTTTGGCCTCGCCCATCGACACCCACACGTCGGTATAGATAAAGTCCGCGCCCTTAAc                                           <  1:2711405/68‑1 (MQ=255)
                               cGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAg                                                               <  1:1730652/49‑1 (MQ=255)
                               cGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAAc                                           <  1:791799/69‑1 (MQ=255)
                               cGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACt                                          <  1:82081/70‑1 (MQ=255)
                                gCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTcc                                        >  1:303929/1‑71 (MQ=255)
                                gCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTcc                                        >  1:2737717/1‑71 (MQ=255)
                                gCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTcc                                        >  1:2096706/1‑71 (MQ=255)
                                   cATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCtt                                     >  1:1258520/1‑71 (MQ=255)
                                    aTTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTc                                    >  1:865566/1‑71 (MQ=255)
                                     tttCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTc                                              <  1:3778258/60‑1 (MQ=255)
                                      ttCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGt                                                        <  1:2784557/49‑1 (MQ=255)
                                       tctcTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAg                                                     >  1:3644837/1‑51 (MQ=255)
                                       tctcTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCaa                                            >  1:271003/1‑60 (MQ=255)
                                       tctcTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTcgc                                  <  1:3294383/70‑1 (MQ=255)
                                           ttttGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGc                                                    >  1:235068/1‑48 (MQ=255)
                                           ttttGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGc                                                    >  1:1968574/1‑48 (MQ=255)
                                           ttttGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTc                                    >  1:3258529/1‑64 (MQ=255)
                                            tttGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTcg                                   >  1:155172/1‑64 (MQ=255)
                                            tttGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATc                            >  1:2388753/1‑71 (MQ=255)
                                            tttGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATc                            >  1:2393502/1‑71 (MQ=255)
                                             ttGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATc                            <  1:731308/70‑1 (MQ=255)
                                               gCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCtt                          <  1:1767907/70‑1 (MQ=255)
                                                cTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTtc                         <  1:3931114/70‑1 (MQ=255)
                                                 ttCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTc                                              <  1:791210/48‑1 (MQ=255)
                                                   cccccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTcgc                                  <  1:1820010/58‑1 (MQ=255)
                                                   cccccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTtcagt                      >  1:95989/1‑70 (MQ=255)
                                                   cccccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTtcagt                      >  1:323326/1‑70 (MQ=255)
                                                   cccccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTtcagt                      >  1:1219262/1‑70 (MQ=255)
                                                   cccccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTtcagt                      >  1:2863978/1‑70 (MQ=255)
                                                   cccccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTtcag                       <  1:2110952/69‑1 (MQ=255)
                                                    tcccATCGACACCCACACGTTGGTATAGATAAAGTCCGCGCCCTTAACGCCTGCCGCCACGTCTtccgt                      <  1:3441947/68‑1 (MQ=255)
                                                    ccccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCt                                      >  1:326320/1‑53 (MQ=255)
                                                     cccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTc                                              <  1:490392/44‑1 (MQ=255)
                                                     cccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCt                                      <  1:1616654/52‑1 (MQ=255)
                                                      ccATCGACACCCACACATCGGTATAGATAAAGTCAGCa                                                   <  1:1177874/38‑1 (MQ=255)
                                                      ccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGc                  >  1:2549709/1‑71 (MQ=255)
                                                      ccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGc                  >  1:3161924/1‑71 (MQ=255)
                                                      ccATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGc                  >  1:2915076/1‑71 (MQ=255)
                                                        aTCGACACCCACACGTCGGTATAGATAAAGTCCGCGCCCTTAACGCCTGCCGCCACGTCTTCCGTCAGAGt                <  1:2063317/71‑1 (MQ=255)
                                                        aTCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGt                <  1:3177021/71‑1 (MQ=255)
                                                         tCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTtcagtc                     >  1:1165605/1‑65 (MQ=255)
                                                         tCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGt                >  1:235799/1‑70 (MQ=255)
                                                          cGACAGCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGAc                               >  1:3020854/1‑54 (MQ=255)
                                                           gACACCCACACGTCGGTATAGATAAAGTCCGCGCCCTTAACGCCTGCCGCCACGTCTTCCGTCAGAGTAat             >  1:1921459/1‑71 (MQ=255)
                                                             cacCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAatat           <  1:3711650/71‑1 (MQ=255)
                                                              acCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAatat           >  1:3902274/1‑70 (MQ=255)
                                                              acCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAata            >  1:1168117/1‑69 (MQ=255)
                                                              acCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATAtt          >  1:3543402/1‑71 (MQ=255)
                                                              acCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATAtt          <  1:1168636/71‑1 (MQ=255)
                                                                ccACACGTCGGTATAGATAAAGTCCGCGCCCTTAACGCCTGCCGCCACGTCTTCCGTCAGAGTAATTTTcc        <  1:2060057/71‑1 (MQ=255)
                                                                ccACACGTCGGTATAGATAAAGTCCGCGCCCTTAACGCCTGCCGCCACGTCTTCCGTCAGAGTAATTTTcc        >  1:3005535/1‑71 (MQ=255)
                                                                ccACACGTCGGTATAGATAAAGTCCGCGCCCTTAACGCCTGCCGCCACGTCTTCCGTCAGAGTAATTTTcc        >  1:3334330/1‑71 (MQ=255)
                                                                 cacacaTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCtt                          <  1:376757/52‑1 (MQ=255)
                                                                  acacaTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCcca      >  1:2699161/1‑71 (MQ=255)
                                                                  acacaTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCcca      >  1:3515815/1‑71 (MQ=255)
                                                                  acacaTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCcca      >  1:1935562/1‑71 (MQ=255)
                                                                  acacaTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCcca      >  1:1314309/1‑71 (MQ=255)
                                                                   cacaTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCccac     >  1:2681229/1‑71 (MQ=255)
                                                                   cacaTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCccac     >  1:355753/1‑71 (MQ=255)
                                                                    acaTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGa                                >  1:2655714/1‑43 (MQ=255)
                                                                    acaTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTtcagt                      <  1:1967672/53‑1 (MQ=255)
                                                                    acaTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCccac     >  1:639797/1‑70 (MQ=255)
                                                                     caTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCccacca   <  1:3089366/71‑1 (MQ=255)
                                                                     caTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCccacca   <  1:3099390/71‑1 (MQ=255)
                                                                      aTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTtca                        <  1:1145214/49‑1 (MQ=255)
                                                                      aTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCCCACCAt  <  1:3451319/71‑1 (MQ=255)
                                                                      aTCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCCCACCAt  <  1:2820243/71‑1 (MQ=255)
                                                                      |                                                                      
CCTGATATTCACGCAGCAATGCAATCCGTTCCGCCCATTTCTCTTTTGCTTCCCCCATCGACACCCACACATCGGTATAGATAAAGTCAGCACCTTCAACTCCCTTCGCGACATCTTCAGTCAGCGTAATATTCCCACCAT  >  minE/2918930‑2919070

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