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
A2 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,321,698 G→A 52.7% T93I (ACC→ATC)  cdh ← CDP‑diacylglycerol phosphotidylhydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,321,6980GA52.7% 8.0 / 166.4 110T93I (ACC→ATC) cdhCDP‑diacylglycerol phosphotidylhydrolase
Reads supporting (aligned to +/- strand):  ref base G (29/23);  new base A (30/28);  total (59/51)
Fisher's exact test for biased strand distribution p-value = 7.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.27e-01

Only 100 of 119 total aligned reads displayed.

TTTTTTGCTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAGTGG  >  minE/2321634‑2321759
                                                                |                                                             
ttttttGCTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATcaac                                                          >  1:2109146/1‑70 (MQ=255)
ttttttGCTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATcaac                                                          >  1:3850185/1‑70 (MQ=255)
         cATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACttt                                                >  1:3672574/1‑71 (MQ=255)
         cATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACttt                                                >  1:1610972/1‑71 (MQ=255)
         cATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACttt                                                >  1:3725904/1‑71 (MQ=255)
          aTAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACttt                                                <  1:1684318/70‑1 (MQ=255)
          aTAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTc                                               <  1:3291532/71‑1 (MQ=255)
          aTAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTc                                               <  1:2168477/71‑1 (MQ=255)
          aTAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTc                                               <  1:3738189/71‑1 (MQ=255)
          aTAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTc                                               <  1:3450397/71‑1 (MQ=255)
          aTAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTc                                               <  1:733938/71‑1 (MQ=255)
          aTAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTc                                               <  1:1197052/71‑1 (MQ=255)
           tAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACttt                                                <  1:1095522/69‑1 (MQ=255)
           tAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATca                                                            <  1:2149672/57‑1 (MQ=255)
           tAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACttt                                                >  1:3158404/1‑69 (MQ=255)
            aaaaTCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGt                                                              >  1:1406940/1‑54 (MQ=255)
            aaaaTCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGt                                                              >  1:3687996/1‑54 (MQ=255)
            aaaaTCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGt                                                              >  1:4001391/1‑54 (MQ=255)
            aaaaTCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGt                                                              >  1:1249686/1‑54 (MQ=255)
             aaaTCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCa                                              >  1:2648547/1‑69 (MQ=255)
             aaaTCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCa                                              >  1:2678968/1‑69 (MQ=255)
             aaaTCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCa                                              >  1:3930185/1‑69 (MQ=255)
             aaaTCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAg                                             >  1:910632/1‑70 (MQ=255)
              aaTCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAgg                                                     <  1:4245841/61‑1 (MQ=255)
                tCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACt                                                  <  1:1102513/62‑1 (MQ=255)
                tCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACt                                                  <  1:2659281/62‑1 (MQ=255)
                tCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTAcc                                         <  1:3950203/71‑1 (MQ=255)
                tCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTAcc                                         <  1:800316/71‑1 (MQ=255)
                 cACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCg                                        >  1:1534483/1‑71 (MQ=255)
                  aCGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACt                                                  <  1:2184736/60‑1 (MQ=255)
                      gcCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAat                                   <  1:2332225/71‑1 (MQ=255)
                         tGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGtt                                      <  1:3816701/65‑1 (MQ=255)
                          gccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacga                               >  1:3713420/1‑71 (MQ=255)
                          gccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGCACTTTCAGTACCGTTAatacga                               >  1:2799086/1‑71 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacga                               >  1:484503/1‑70 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacga                               >  1:2417723/1‑70 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacg                                >  1:1283836/1‑69 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatac                                 <  1:2034026/68‑1 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAatacga                               >  1:262528/1‑70 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAatacga                               >  1:4240471/1‑70 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAatacga                               >  1:970456/1‑70 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAatacga                               >  1:3765700/1‑70 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAatacga                               >  1:564398/1‑70 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAatac                                 >  1:2129680/1‑68 (MQ=255)
                           ccaagccaaCCAAAAGAAGTTCCGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacga                               >  1:3049236/1‑70 (MQ=255)
                               gccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGt                          >  1:3513287/1‑71 (MQ=255)
                               gccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGt                          >  1:1514534/1‑71 (MQ=255)
                               gccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGt                          >  1:1616160/1‑71 (MQ=255)
                                ccaaccaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGtt                         <  1:3809567/71‑1 (MQ=255)
                                ccaaccaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGtt                         <  1:3215718/71‑1 (MQ=255)
                                ccaaccaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGtt                         <  1:1763087/71‑1 (MQ=255)
                                ccaaccaaAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGtt                         <  1:1235436/71‑1 (MQ=255)
                                 caaccaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGtt                         <  1:3676346/70‑1 (MQ=255)
                                   accaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTgg                       >  1:2843417/1‑70 (MQ=255)
                                   accaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTgg                       >  1:2620034/1‑70 (MQ=255)
                                   accaaAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTc                                               <  1:3903347/46‑1 (MQ=255)
                                   accaaAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTc                                               <  1:347217/46‑1 (MQ=255)
                                   accaaAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTc                                               <  1:3815085/46‑1 (MQ=255)
                                   accaaAAGAAGTTCGGCGTTGAAGGATAGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTgg                       >  1:2833146/1‑70 (MQ=255)
                                    ccaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCa                     <  1:65421/71‑1 (MQ=255)
                                      aaaaGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTa                                           >  1:2741290/1‑47 (MQ=255)
                                      aaaaGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTa                                           >  1:34854/1‑47 (MQ=255)
                                      aaaaGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTa                                           >  1:865586/1‑47 (MQ=255)
                                      aaaaGAAGTTCGGCGTTGAAGGATCGGT‑AACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATc                   >  1:734143/1‑70 (MQ=255)
                                       aaaGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAg                                             <  1:1948794/44‑1 (MQ=255)
                                       aaaGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatac                                 <  1:4167901/56‑1 (MQ=255)
                                       aaaGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatac                                 <  1:1953133/56‑1 (MQ=255)
                                       aaaGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatac                                 <  1:1012201/56‑1 (MQ=255)
                                         agaagTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCaa                 >  1:3602988/1‑70 (MQ=255)
                                         agaagTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCaa                 >  1:606638/1‑70 (MQ=255)
                                           aagTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCaa                 >  1:1068271/1‑68 (MQ=255)
                                            agTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCaa                 >  1:1517602/1‑67 (MQ=255)
                                                 ggCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTg        <  1:94823/71‑1 (MQ=255)
                                                 ggCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTg        <  1:2198242/71‑1 (MQ=255)
                                                  gCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGc       <  1:1374227/71‑1 (MQ=255)
                                                  gCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGc       <  1:900530/71‑1 (MQ=255)
                                                  gCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTg        >  1:2172065/1‑70 (MQ=255)
                                                  gCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGc       <  1:1411492/71‑1 (MQ=255)
                                                     ttGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTgtc                      <  1:2996495/53‑3 (MQ=255)
                                                     ttGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGc                      <  1:1427184/53‑1 (MQ=255)
                                                     ttGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCaa                 >  1:746234/1‑58 (MQ=255)
                                                       gAAGGATCGATCAACAAAGGACTTTCAGTACCGtt                                      <  1:3834884/35‑1 (MQ=255)
                                                       gAAGGATCGATCAACAAAGGACTTTCAGTACCGtt                                      <  1:1915393/35‑1 (MQ=255)
                                                       gAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCAt                    >  1:2873875/1‑53 (MQ=255)
                                                       gAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCAt                    >  1:804589/1‑53 (MQ=255)
                                                       gAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCAt                    >  1:2059273/1‑53 (MQ=255)
                                                       gAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCAt                    >  1:3747364/1‑53 (MQ=255)
                                                       gAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGCCAt                    >  1:3369507/1‑53 (MQ=255)
                                                         aGGATCGATCAACAAAGGACTTTCAGTACCGTTaa                                    <  1:1739578/35‑1 (MQ=255)
                                                         aGGATCGATCAACAAAGGACTTTCAGTACCGTTaa                                    <  1:1292618/35‑1 (MQ=255)
                                                           gatcgatcAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCaa                 >  1:2451054/1‑52 (MQ=255)
                                                           gatcgatcAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCaa                 >  1:3862095/1‑52 (MQ=255)
                                                           gatcgatcAACAAAGGACTTTCAGTAACGTTAATACGATACGTTGGCATCaa                 >  1:689085/1‑52 (MQ=255)
                                                             tCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGata           <  1:1272965/56‑1 (MQ=255)
                                                             tCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGCCATCAACAGata           <  1:2387377/56‑1 (MQ=39)
                                                                gTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACa               <  1:1428253/49‑1 (MQ=255)
                                                                gTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACa               <  1:4071531/49‑1 (MQ=255)
                                                                gTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACa               <  1:3894173/49‑1 (MQ=255)
                                                                gTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACa               <  1:1071645/49‑1 (MQ=255)
                                                                gTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat            <  1:2200761/52‑1 (MQ=255)
                                                                |                                                             
TTTTTTGCTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAGTGG  >  minE/2321634‑2321759

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