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 832,277 C→T 39.2% Y245Y (TAC→TAT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,2770CT39.2% 75.3 / 103.0 102Y245Y (TAC→TAT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (33/29);  new base T (20/20);  total (53/49)
Fisher's exact test for biased strand distribution p-value = 8.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

Only 100 of 104 total aligned reads displayed.

CGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTT  >  minE/832208‑832345
                                                                     |                                                                    
cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTAc                                                                      <  1:1238824/70‑1 (MQ=255)
cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTAc                                                                      <  1:3566441/70‑1 (MQ=255)
cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACa                                                                     <  1:945171/71‑1 (MQ=255)
cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACa                                                                     <  1:4997379/71‑1 (MQ=255)
  aCTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAAc                                                                   >  1:3771725/1‑71 (MQ=255)
    ttGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTc                                                                 >  1:418955/1‑71 (MQ=255)
       cctcctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAg                                                              >  1:2857378/1‑71 (MQ=255)
           ctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTa                                                           >  1:3282601/1‑70 (MQ=255)
           ctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTa                                                           >  1:5526511/1‑70 (MQ=255)
           ctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGATa                                                           >  1:2386521/1‑70 (MQ=255)
              cGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAcat                                                        >  1:5357351/1‑70 (MQ=255)
                  tcCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCg                                                   >  1:1374314/1‑71 (MQ=255)
                    cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACatcatc                                                    <  1:4710229/68‑1 (MQ=255)
                    cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACatcatc                                                    <  1:1900274/68‑1 (MQ=255)
                    cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACatcatc                                                    <  1:3833639/68‑1 (MQ=255)
                    cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGcc                                                 <  1:5186408/71‑1 (MQ=255)
                    cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGcc                                                 <  1:3036599/71‑1 (MQ=255)
                      atgaCCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTg                                               >  1:1306513/4‑71 (MQ=255)
                        gaCCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTggg                                             >  1:3806285/2‑71 (MQ=255)
                        gaCCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTga                                              <  1:3316019/69‑2 (MQ=255)
                           cTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGt                                          >  1:3091976/1‑71 (MQ=255)
                            tGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGc                                                  >  1:5623445/1‑62 (MQ=255)
                             ggggCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGc                                                             >  1:5555730/1‑50 (MQ=255)
                              gggCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCa                                        >  1:2219594/1‑70 (MQ=255)
                              gggCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTct                                        <  1:3094541/70‑2 (MQ=255)
                              gggCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTct                                        >  1:1850287/1‑69 (MQ=255)
                                gCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTg                                               <  1:1357902/61‑1 (MQ=255)
                                  gAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGt                                   <  1:4493414/71‑1 (MQ=255)
                                    gCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGc                                 <  1:383673/71‑1 (MQ=255)
                                    gCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCg                                                   <  1:463908/53‑1 (MQ=38)
                                    gCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGtac                                 <  1:120337/71‑3 (MQ=255)
                                       aaCTGACGTACTGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCg                               >  1:2519185/1‑70 (MQ=255)
                                       aaCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCg                               >  1:3401781/1‑70 (MQ=255)
                                        accgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                               >  1:468365/4‑69 (MQ=255)
                                        accgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCa                             <  1:5522420/68‑1 (MQ=255)
                                        aCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCa                             <  1:2961473/71‑1 (MQ=255)
                                         ccgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCt                                                >  1:2336842/3‑51 (MQ=38)
                                         ccgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCt                                                >  1:2343359/3‑51 (MQ=38)
                                         ccgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCt                                                >  1:565916/3‑51 (MQ=38)
                                         cTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCt                                                >  1:520417/1‑51 (MQ=255)
                                          tGACGTACCGGAATCTGCTGACTGGTACAACTCCa                                                               <  1:5091767/35‑1 (MQ=255)
                                          tGACGTACCGGAATCTGCTGACTGGTACAACTCCa                                                               <  1:5598279/35‑1 (MQ=255)
                                          tGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTgggg                                            <  1:3502929/54‑1 (MQ=255)
                                          tGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACg                                    >  1:3295964/1‑62 (MQ=255)
                                          tGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACg                                    >  1:170113/1‑62 (MQ=255)
                                          cgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                           >  1:1384451/2‑71 (MQ=255)
                                           gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                           >  1:5269461/1‑70 (MQ=255)
                                           gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                           >  1:781607/1‑70 (MQ=255)
                                           gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                           >  1:1956245/1‑70 (MQ=255)
                                           gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGAc                          <  1:4100523/71‑1 (MQ=255)
                                            aCGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGAcg                         >  1:2852621/1‑71 (MQ=255)
                                                aCCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                               <  1:3213199/61‑1 (MQ=255)
                                                 ccGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAc                    >  1:2828340/1‑71 (MQ=255)
                                                  cGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGAcgcg                       <  1:3832576/67‑1 (MQ=255)
                                                  cGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                               <  1:1970589/59‑1 (MQ=38)
                                                   ggAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                               <  1:4413453/58‑1 (MQ=38)
                                                    gAATCTGCTGACTGGTACAACTCCAGCTACATCATCg                                                   >  1:3247520/1‑37 (MQ=255)
                                                    gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGc                                                  >  1:3921026/1‑38 (MQ=255)
                                                    gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGc                                                  >  1:1041930/1‑38 (MQ=255)
                                                    gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc                 >  1:676253/1‑71 (MQ=255)
                                                    gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc                 >  1:2135068/1‑71 (MQ=255)
                                                    gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcc                   >  1:3576965/1‑69 (MQ=255)
                                                    gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCtaa                                      >  1:938377/1‑50 (MQ=38)
                                                    gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCtaa                                      >  1:2442026/1‑50 (MQ=38)
                                                    gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCtaa                                      >  1:2908903/1‑50 (MQ=38)
                                                    gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAcgcc                 <  1:935558/71‑1 (MQ=255)
                                                    gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAcgcc                 <  1:878330/71‑1 (MQ=255)
                                                     aaTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGt                      <  1:5454331/65‑1 (MQ=255)
                                                     aaTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGt                      <  1:2089654/65‑1 (MQ=255)
                                                      aTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCgg               <  1:3040704/71‑1 (MQ=255)
                                                       tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                                       <  1:2711814/46‑1 (MQ=255)
                                                       tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                                       <  1:251050/46‑1 (MQ=255)
                                                       tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                                       <  1:519489/46‑1 (MQ=255)
                                                       tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc                    >  1:166102/1‑65 (MQ=255)
                                                       tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc                    >  1:127842/1‑65 (MQ=255)
                                                       tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc                    >  1:240491/1‑65 (MQ=255)
                                                        ctgctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGAt             >  1:2694472/1‑71 (MQ=255)
                                                         tgctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATg            >  1:4384016/1‑71 (MQ=255)
                                                         tgccgACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGacg            >  1:3068280/1‑69 (MQ=255)
                                                          gctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGAt             >  1:1039279/1‑69 (MQ=255)
                                                            tgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                                       <  1:3941471/41‑1 (MQ=255)
                                                            tgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                                       <  1:2425721/41‑1 (MQ=255)
                                                            tgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                                       <  1:5640793/41‑1 (MQ=255)
                                                              aCTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAAc                                     >  1:1631243/1‑41 (MQ=255)
                                                                tGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCAct      >  1:3605696/1‑70 (MQ=255)
                                                                 ggTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                               >  1:1345933/1‑44 (MQ=255)
                                                                 ggTACAACTCCAGCTACATCATCGCCTGGGGGGCAAACGTGCCGCAGACGCGTACCCCGGATGCTCAct      <  1:350138/69‑1 (MQ=255)
                                                                  gTATAACTCCAGTTACATCATCGCCTGGGGGTCTAACGta                                  <  1:4712597/40‑2 (MQ=37)
                                                                  gTATAACTCCAGTTACATCATCGCCTGGGGGTCTAACGta                                  <  1:4514718/40‑2 (MQ=37)
                                                                  gTATAACTCCAGTTACATCATCGCCTGGGGGTCTAACGta                                  <  1:5528778/40‑2 (MQ=37)
                                                                  gTATAACTCCAGTTACATCATCGCCTGGGGGTCTAACGta                                  <  1:429448/40‑2 (MQ=37)
                                                                  gTATAACTCCAGTTACATCATCGCCTGGGGGTCTAACGta                                  <  1:422803/40‑2 (MQ=37)
                                                                  gTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCActtct   >  1:3538926/1‑71 (MQ=255)
                                                                  gTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCActtc    <  1:3426758/70‑1 (MQ=255)
                                                                  gTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCa                             <  1:2813539/45‑1 (MQ=255)
                                                                  gTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCActt     <  1:1521/69‑1 (MQ=255)
                                                                   tACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc                 <  1:853902/56‑1 (MQ=255)
                                                                   tACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc                 <  1:5281022/56‑1 (MQ=255)
                                                                   tACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCActtctt  <  1:2389662/71‑1 (MQ=255)
                                                                    aCAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCActtctt  >  1:5534822/1‑70 (MQ=255)
                                                                     |                                                                    
CGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTT  >  minE/832208‑832345

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