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 832,220 T→C 22.1% P226P (CCT→CCC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,2200TC22.1% 148.4 / 39.6 77P226P (CCT→CCC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (29/31);  new base C (8/9);  total (37/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GTGCACGCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAC  >  minE/832150‑832289
                                                                      |                                                                     
gTGCACGCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGTTTCTACGACTGGTACTGCGACTTGcctcct                                                                       <  1:2330743/71‑1 (MQ=255)
   cACGCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCg                                                                    >  1:2483430/1‑71 (MQ=255)
   cACGCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCg                                                                    >  1:2843832/1‑71 (MQ=255)
   cACGCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCg                                                                    <  1:2010019/71‑1 (MQ=255)
   cACGCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCg                                                                    >  1:1408826/1‑71 (MQ=255)
     cGCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtc                                                                  >  1:1970190/1‑71 (MQ=255)
     cGCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtc                                                                  <  1:1525087/71‑1 (MQ=255)
      gCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtct                                                                 >  1:1003353/1‑71 (MQ=255)
      gCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtct                                                                 >  1:3162483/1‑71 (MQ=255)
      gCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtct                                                                 >  1:3778550/1‑71 (MQ=255)
      gCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtct                                                                 >  1:510064/1‑71 (MQ=255)
      gCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtc                                                                  >  1:2269785/1‑70 (MQ=255)
       cTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtctc                                                                <  1:1105305/71‑1 (MQ=255)
         aTCTGTCGCTGCTTGGCGGCACCTGTTTAAGTTTCTACGACTGGTATTGCGACCTGccgcccgc                                                                     >  1:3501843/1‑64 (MQ=255)
         aTCTGTCGCTGCTTGGCGGCACCTGTTTAAGTTTCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGcc                                                               <  1:2645165/70‑1 (MQ=255)
         aTCTGTCGCTGCTTGGCGGCACCTGTTTAAGTTTCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGcc                                                               >  1:3292544/1‑70 (MQ=255)
          tctgtcGCTGCTTGGCGGCACCTGTTTAAGTTTCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGcc                                                               <  1:3875853/69‑1 (MQ=255)
           ctctcGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGc                                                             >  1:2059903/1‑70 (MQ=255)
           ctctcGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGc                                                             >  1:1034909/1‑70 (MQ=255)
           ctctcGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGc                                                             >  1:1599583/1‑70 (MQ=255)
             gtcGCTGCTTGGCGGCACCTGTTTAAGTTTCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCgat                                                            >  1:214126/2‑67 (MQ=255)
              tcGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCaa                                                           <  1:2128473/69‑1 (MQ=255)
              tcGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAAc                                                         >  1:3680238/1‑71 (MQ=255)
              tcGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAAc                                                         >  1:2177040/1‑71 (MQ=255)
                gCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtctc                                                                <  1:3811769/62‑1 (MQ=255)
                 cTGATTGGCTGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTg                                                      <  1:3590913/71‑1 (MQ=255)
                 cTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTg                                                      <  1:1659438/71‑1 (MQ=255)
                   gATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTggg                                                    >  1:1951126/1‑71 (MQ=255)
                    aTTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTgggg                                                   >  1:3435915/1‑71 (MQ=255)
                     ttGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGc                                                  <  1:3029009/71‑1 (MQ=255)
                     ttGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGc                                                  >  1:2810613/1‑71 (MQ=255)
                      ttgCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCg                                                 <  1:3865011/69‑1 (MQ=255)
                        gCGGTACTTGCTTAAGCTTCTACGACTGGTACAGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAg                                               <  1:2912485/71‑1 (MQ=255)
                        gCGGCACCTGTTTAAGTTTCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAg                                               >  1:1652358/1‑71 (MQ=255)
                          ggTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCa                                                            >  1:2643338/1‑56 (MQ=255)
                           gTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCa                                             >  1:3821945/1‑70 (MQ=255)
                            tACTTGCTTAAGCTTCTACGACTCGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTggg                                                    <  1:869607/62‑1 (MQ=255)
                              cTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACt                                         <  1:3917703/71‑1 (MQ=255)
                               ttGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCaaa                                                          >  1:2709945/1‑53 (MQ=255)
                                tGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtct                                                                 >  1:247265/1‑45 (MQ=255)
                                 gCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTg                                        <  1:700467/69‑1 (MQ=255)
                                  cTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTg                                        <  1:1064268/68‑1 (MQ=255)
                                  cTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACg                                     <  1:1482933/71‑1 (MQ=255)
                                    tAAGTTTCTACGACTGGTATTGCGACCTGccgcccgc                                                                     >  1:247908/1‑37 (MQ=16)
                                    tAAGTTTCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTa                                   >  1:1842024/1‑71 (MQ=255)
                                     aaGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtct                                                                 <  1:824904/40‑1 (MQ=255)
                                       gCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtctc                                                                >  1:824643/1‑39 (MQ=255)
                                       gCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGtct                                                                 <  1:2590855/38‑1 (MQ=255)
                                       gCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTcc                                                               >  1:81729/1‑40 (MQ=255)
                                       gCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTcc                                                               >  1:2858709/1‑40 (MQ=255)
                                        cTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCTCAAACCTGGGGCGAGCAAACTGACGTACCgg                               <  1:375734/71‑1 (MQ=255)
                                        cTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTg                                                      <  1:1304482/48‑1 (MQ=255)
                                          tCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGc                                                  <  1:1338106/50‑1 (MQ=255)
                                          tCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCa                                             <  1:3075661/55‑1 (MQ=255)
                                          tCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGa                              <  1:3881838/70‑1 (MQ=255)
                                          tCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGa                              >  1:2231834/1‑70 (MQ=255)
                                          tCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGaa                             >  1:902386/1‑71 (MQ=255)
                                           cTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCaa                                                           <  1:2584082/40‑1 (MQ=255)
                                           cTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCaa                                                           <  1:3819244/40‑1 (MQ=255)
                                           cTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGa                              <  1:877986/69‑1 (MQ=255)
                                           cTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAAt                            >  1:1349517/1‑71 (MQ=255)
                                            tACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGa                                                >  1:2636449/1‑50 (MQ=255)
                                            tACGACTGGTATTGCGACCTGCCGCCCGCATCGCCGATGACCTGGGGCg                                                 <  1:2179961/49‑1 (MQ=255)
                                             aCGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAAt                            >  1:3906156/1‑69 (MQ=255)
                                              cGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATctg                         >  1:2893140/1‑71 (MQ=255)
                                              cGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATct                          <  1:3163374/70‑1 (MQ=255)
                                              cGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAAt                            <  1:3273029/68‑1 (MQ=255)
                                                 cTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCg                                                 <  1:2402401/44‑1 (MQ=255)
                                                 cTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATctgctg                      <  1:2482226/71‑1 (MQ=255)
                                                      attGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATctgc                        <  1:3019215/62‑1 (MQ=255)
                                                      attGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTgg                 >  1:1164402/3‑71 (MQ=255)
                                                        tGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGa                              <  1:3892563/56‑1 (MQ=255)
                                                         gCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGa                              <  1:3828782/55‑1 (MQ=255)
                                                         gCGACTTGCCTCATGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTa               >  1:1000755/1‑70 (MQ=255)
                                                          cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTAc              <  1:1217644/70‑1 (MQ=255)
                                                          cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTAc              <  1:3645032/70‑1 (MQ=255)
                                                          cGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTat              <  1:3768923/70‑2 (MQ=255)
                                                              ttGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTc         >  1:2335376/1‑71 (MQ=255)
                                                                gCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTgg                 <  1:2292016/61‑1 (MQ=255)
                                                                gCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTgg                 <  1:313955/61‑1 (MQ=255)
                                                                 cctcctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCa       >  1:1639362/1‑70 (MQ=255)
                                                                   tcctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCa       <  1:2338139/68‑1 (MQ=255)
                                                                   tcctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCa       <  1:2042996/68‑1 (MQ=255)
                                                                     ctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAc  <  1:2468480/71‑1 (MQ=255)
                                                                      |                                                                     
GTGCACGCTATCTCTCGCTGATTGGCGGTACTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAC  >  minE/832150‑832289

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