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 1,934,155 C→T 26.8% Q96Q (CAG→CAA)  lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,934,1550CT26.8% 184.7 / 71.7 116Q96Q (CAG→CAA) lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base C (40/44);  new base T (29/2);  total (70/46)
Fisher's exact test for biased strand distribution p-value = 3.30e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

Only 100 of 116 total aligned reads displayed.

GCCGAGGTCCCATTTTTTGAACTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGTCATCAT  >  minE/1934086‑1934223
                                                                     |                                                                    
    aGGTCCCATTTTTTGAACTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAAt                                                                 <  1:201982/71‑1 (MQ=255)
      gTCCCATTTTTTGAACTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGc                                                               >  1:1882190/1‑71 (MQ=255)
      atCCCATTTTTTAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAAtac                                                               <  1:2274131/70‑3 (MQ=255)
        cccATTTTTTAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGaa                                                                  >  1:506938/1‑66 (MQ=255)
           aTTTTTTGAACTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGAc                                                            >  1:296627/1‑69 (MQ=255)
           aTTTTTTGAACTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCg                                                          >  1:2943895/1‑71 (MQ=255)
           aTTTTTTGAACTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCg                                                          >  1:2809910/1‑71 (MQ=255)
           aTTTTTTAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTg                                                                    >  1:3025360/1‑61 (MQ=255)
           aTTTTTTAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTg                                                                    >  1:2434866/1‑61 (MQ=255)
           aTTTTTTAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTg                                                                    >  1:4410789/1‑61 (MQ=255)
           aTTTTTTAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAATACGGcca                                                          >  1:3405972/1‑70 (MQ=255)
           aTTTTTTAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAATACGGcca                                                          >  1:2388906/1‑70 (MQ=255)
             tttttGAACTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGc                                                         >  1:418436/1‑70 (MQ=255)
             tttttAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAATACGGCCAcc                                                        >  1:530027/1‑71 (MQ=255)
              ttttAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGaa                                                                  >  1:4156094/1‑60 (MQ=255)
              ttttAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAAtac                                                               >  1:1574154/1‑61 (MQ=255)
              ttttAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAAta                                                                >  1:4884008/1‑61 (MQ=255)
              ttttAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAAta                                                                >  1:706701/1‑61 (MQ=255)
              ttttAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAATACGGcc                                                           >  1:4939613/1‑67 (MQ=255)
              ttttAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAATACGGCCAcc                                                        >  1:3243048/1‑70 (MQ=255)
              ttttAAACTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAATACGGCCAcc                                                        >  1:3316314/1‑70 (MQ=255)
               tttGAACTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCa                                                       <  1:2318093/70‑1 (MQ=255)
                 taaaCTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAATACGGCCACCGAca                                                    >  1:3441751/3‑70 (MQ=255)
                 taaaCTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAATACGGCCACCGAca                                                    >  1:2601234/3‑70 (MQ=255)
                  gAACTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACg                                                    <  1:1604905/70‑1 (MQ=255)
                   aaCTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTc                                                  <  1:2636232/71‑1 (MQ=255)
                    aCTGATCGTTATAAACACCTTCTGGCAGGCTATCTCTTGCAACGTACAGTTGAATACGGCCACCGACATcc                                                 >  1:3362005/1‑71 (MQ=255)
                        cTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTg                                               <  1:2561669/69‑1 (MQ=255)
                        cTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCa                                             <  1:3604473/71‑1 (MQ=255)
                          cGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAgg                                           >  1:4000042/1‑71 (MQ=255)
                           gTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAggg                                          >  1:3317548/1‑71 (MQ=255)
                           gTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAggg                                          <  1:1469185/71‑1 (MQ=255)
                             tataAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGc                                              <  1:4041612/65‑1 (MQ=255)
                             tataAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGt                                         >  1:218029/1‑70 (MQ=255)
                             tataAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGt                                         >  1:4648808/1‑70 (MQ=255)
                              ataAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCt                                                                     >  1:2273053/1‑41 (MQ=255)
                              ataAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTaa                                       >  1:3361187/1‑71 (MQ=255)
                              ataAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTaa                                       >  1:4515001/1‑71 (MQ=255)
                                aaaCGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATg                                                                <  1:3328117/44‑1 (MQ=255)
                                 aaCGCCTTCCGGGAGATCGTCACGGGCAACGTCCAGCTGAATGCGACCGCCa                                                       >  1:1493144/1‑52 (MQ=255)
                                   cGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTc                                                  >  1:1558446/1‑55 (MQ=255)
                                       ttCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCg                                                              <  1:3309639/39‑1 (MQ=255)
                                       ttCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCg                                                              <  1:4397086/39‑1 (MQ=255)
                                       ttCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCg                                                              <  1:876855/39‑1 (MQ=255)
                                       ttCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGc                                              <  1:3751635/55‑1 (MQ=255)
                                        tCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGa                                                             >  1:2600601/1‑39 (MQ=255)
                                        tCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGa                                                             >  1:1827217/1‑39 (MQ=255)
                                        tCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGc                             >  1:2419192/1‑71 (MQ=255)
                                         ccGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGAc                                                            >  1:30936/1‑39 (MQ=255)
                                         ccGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGAc                                                            >  1:4034452/1‑39 (MQ=255)
                                         ccGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGc                             <  1:315032/70‑1 (MQ=255)
                                         ccGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCt                            >  1:43532/1‑71 (MQ=255)
                                         ccGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCt                            >  1:830366/1‑71 (MQ=255)
                                         ccGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCt                            >  1:3594207/1‑71 (MQ=255)
                                           gggAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCttt                          <  1:2600185/71‑1 (MQ=255)
                                            ggAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTa                         <  1:4818060/71‑1 (MQ=255)
                                               gaTCGTCACGGGCAACGTACAGCTGAATGCGACCGcc                                                        >  1:3085563/1‑37 (MQ=255)
                                                 tCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCat                    <  1:3923450/71‑1 (MQ=255)
                                                 tCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCat                    <  1:1369846/71‑1 (MQ=255)
                                                    tCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCataat                 <  1:4953092/71‑1 (MQ=255)
                                                    tCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCat                    <  1:4254397/68‑1 (MQ=255)
                                                    tCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCat                    <  1:1506555/68‑1 (MQ=255)
                                                    tCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCat                    <  1:1500069/68‑1 (MQ=255)
                                                     cACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAgg                                           >  1:5028445/1‑44 (MQ=255)
                                                     cACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAgg                                           >  1:2967745/1‑44 (MQ=255)
                                                     cACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGa                                >  1:3729867/1‑55 (MQ=255)
                                                      aCGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATac               >  1:5635555/1‑71 (MQ=255)
                                                      aCGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATac               >  1:4089260/1‑71 (MQ=255)
                                                      aCGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATac               >  1:5192515/1‑71 (MQ=255)
                                                      aCGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATac               >  1:2305793/1‑71 (MQ=255)
                                                      aCGGGCAACGTACAGATGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCataa                  >  1:2103692/1‑68 (MQ=255)
                                                       cttgCAACGTACAGTTGAATACGGCCACCGACATCCTGCAACGTTACAAAGGAGGCTTTCCCCATGATac               >  1:4010170/4‑70 (MQ=255)
                                                       cGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGa                                    <  1:5206876/49‑1 (MQ=255)
                                                       cGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGa                                    <  1:1083991/49‑1 (MQ=255)
                                                       cGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGa                                    <  1:5608964/49‑1 (MQ=255)
                                                       cGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGa                                    <  1:3553945/49‑1 (MQ=255)
                                                       cGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATac               >  1:5431537/1‑70 (MQ=255)
                                                        ttgCAACGTACAGTTGAATACGGCCACCGACATCCTGCAACGTTACAAAGGAGGCTTTCCCCATGATacga             >  1:1882957/3‑71 (MQ=255)
                                                          gCAACGTACAGTTGAATACGGCCACCGACATCCTGCAACGTTACAAAGGAGGCTTTccc                       >  1:2435601/1‑59 (MQ=255)
                                                          gCAACGTACAGTTGAATACGGCCACCGACATCCTGCAACGTTACAAAGGAGGCTTTccc                       >  1:3486407/1‑59 (MQ=255)
                                                          gCAACGTACAGTTGAATACGGCCACCGACATCCTGCAACGTTACAAAGGAGGCTTTCCCCATGATacga             >  1:97317/1‑69 (MQ=255)
                                                           cAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATACGACgg          >  1:1178934/1‑71 (MQ=255)
                                                            aaCGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCa                     <  1:1086633/59‑1 (MQ=255)
                                                             aCGTACAGTTGAATACGGCCACCGACATCCTGCAACGTTACAAAGGAGGCTTTCCCCATGATACGACGGGt        >  1:3189115/1‑71 (MQ=255)
                                                             aCGTACAGTTGAATACGGCCACCGACATCCTGCAACGTTACAAAGGAGGCTTTCCCCATGATACGACGGGt        >  1:1821742/1‑71 (MQ=255)
                                                             aCGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGt        <  1:1442921/71‑1 (MQ=255)
                                                              cGTACAGTTGAATACGGCCACCGACATCCTGCAACGTTACAAAGGAGGCTTTCCCCATGATACGACGGGt        >  1:2923742/1‑70 (MQ=255)
                                                               gTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGaaa                                  <  1:4147612/43‑1 (MQ=255)
                                                               gTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGaaa                                  <  1:2922051/43‑1 (MQ=255)
                                                               gTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGa                                    <  1:5027833/41‑1 (MQ=255)
                                                               gTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGtca      <  1:2699140/71‑1 (MQ=255)
                                                                tACAGTTGAATACGGCCACCGACATCCTGCAACGTTACAAAGGAGGCTTTCCCCATGATACGACGGGtcat     <  1:459105/71‑1 (MQ=255)
                                                                tACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACg                              <  1:3633276/46‑1 (MQ=255)
                                                                tACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGtcat     <  1:192176/71‑1 (MQ=255)
                                                                tACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGtcat     >  1:2695632/1‑71 (MQ=255)
                                                                 aCAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATacg              >  1:1351298/1‑61 (MQ=255)
                                                                  cAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGaa                                   >  1:256010/1‑39 (MQ=255)
                                                                  cAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGtcatca   >  1:2369524/1‑71 (MQ=255)
                                                                  cAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGtcatc    <  1:5568952/70‑1 (MQ=255)
                                                                   aGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGTcatcat  <  1:4756993/71‑1 (MQ=255)
                                                                     |                                                                    
GCCGAGGTCCCATTTTTTGAACTGCTCGTTATAAACGCCTTCCGGGAGATCGTCACGGGCAACGTACAGCTGAATGCGACCGCCAACGTCCTGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGTCATCAT  >  minE/1934086‑1934223

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