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
A108 F1 I1 R1 80 195.1 12639756 93.3% 11792892 75.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 3,011,220 T→C intergenic (+191/+47) ECB_02811 → / ← ECB_02812 conserved hypothetical protein/conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6063,011,2200TC97.7% 544.1 / ‑0.3 132intergenic (+191/+47)ECB_02811/ECB_02812conserved hypothetical protein/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (2/1);  new base C (70/59);  total (72/60)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

Only 100 of 157 total aligned reads displayed.

CCGAGTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAATAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACAAAA  >  REL606/3011147‑3011292
                                                                         |                                                                        
ccGAGTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATataaaacaa                                                                        <  2:4496672/76‑1 (MQ=255)
ccGAGTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATataaaacaa                                                                        >  1:3403466/1‑76 (MQ=255)
 cGAGTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATataaaacaaa                                                                       >  2:2593702/1‑76 (MQ=255)
 cGAGTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATataaaacaaa                                                                       <  2:1503934/76‑1 (MQ=255)
 cGAGTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATataaaacaaa                                                                       >  1:3774515/1‑76 (MQ=255)
 cGAGTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATataaaacaaa                                                                       >  1:2557532/1‑76 (MQ=255)
   aGTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACt                                                                     <  2:3440952/76‑1 (MQ=255)
    gTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACtt                                                                    >  2:6108962/1‑76 (MQ=255)
    gTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACtt                                                                    <  1:956316/76‑1 (MQ=255)
    gTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACtt                                                                    >  2:4212549/1‑76 (MQ=255)
       cGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTggg                                                                 >  1:4255114/1‑76 (MQ=255)
       cGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTggg                                                                 >  2:1835742/1‑76 (MQ=255)
          caccacTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGc                                                              <  1:3965514/76‑1 (MQ=255)
            ccacTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCAt                                                            <  1:977980/76‑1 (MQ=255)
             cacTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATa                                                           <  1:3776350/76‑1 (MQ=255)
              acTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATaa                                                          >  2:1115214/1‑76 (MQ=255)
               cTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAAc                                                         <  2:1019409/76‑1 (MQ=255)
                tAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACg                                                        <  2:1638303/76‑1 (MQ=255)
                 aaTTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGc                                                       >  1:4393092/1‑76 (MQ=255)
                 aaTTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGc                                                       >  1:3912056/1‑76 (MQ=255)
                  aTTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGcc                                                      >  2:334837/1‑76 (MQ=255)
                   ttCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCa                                                     >  1:5962624/1‑76 (MQ=255)
                   ttCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCa                                                     <  1:6227428/76‑1 (MQ=255)
                    tCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCAt                                                    >  1:4998194/1‑76 (MQ=255)
                    tCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCAt                                                    <  2:1495859/76‑1 (MQ=255)
                    tCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCAt                                                    <  1:1437891/76‑1 (MQ=255)
                      ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCa                                                  <  2:454172/76‑1 (MQ=255)
                      ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCa                                                  <  1:2577069/76‑1 (MQ=255)
                      ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCa                                                  >  2:2462474/1‑76 (MQ=255)
                      ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCa                                                  >  2:3342892/1‑76 (MQ=255)
                       tAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAg                                                 >  2:1989045/1‑76 (MQ=255)
                        aaGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAgg                                                <  2:5161470/76‑1 (MQ=255)
                        aaGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAgg                                                >  2:4952995/1‑76 (MQ=255)
                        aaGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAgg                                                >  2:2321608/1‑76 (MQ=255)
                        aaGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAgg                                                <  1:5924488/76‑1 (MQ=255)
                         aGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGt                                               >  2:3057584/1‑76 (MQ=255)
                         aGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGt                                               >  2:75356/1‑76 (MQ=255)
                              ccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTaa                                          >  1:4762291/1‑76 (MQ=255)
                               cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTaaa                                         >  2:4668405/1‑76 (MQ=255)
                               cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTaaa                                         <  1:2987293/76‑1 (MQ=255)
                                    acaAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTc                                    <  2:184480/76‑1 (MQ=255)
                                      aaGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTccc                                  >  2:2259172/1‑76 (MQ=255)
                                      aaGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTccc                                  >  2:2275333/1‑76 (MQ=255)
                                      aaGGCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTccc                                  >  1:2845575/1‑76 (MQ=255)
                                         gCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGaa                               <  1:1095000/76‑1 (MQ=255)
                                         gCGGGTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGaa                               <  2:5351556/76‑1 (MQ=255)
                                           gggTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAatc                             <  1:5093468/76‑1 (MQ=255)
                                           gggTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAatc                             <  1:2926637/76‑1 (MQ=255)
                                            ggTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAatca                            <  2:5790408/76‑1 (MQ=255)
                                             gTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAatcat                           >  2:156680/1‑76 (MQ=255)
                                             gTTTTTGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAatcat                           >  2:3671026/1‑76 (MQ=255)
                                               ttttGCTTTTGGATCTTTATATAAAATAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAAtcatca                         >  1:4055598/1‑76 (MQ=255)
                                               ttttGCTTTTGGATCTTTATATAAAATAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAAtcatca                         >  2:1261285/1‑76 (MQ=255)
                                               ttttGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAAtcatca                         >  1:413923/1‑76 (MQ=255)
                                               ttttGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAAtcatca                         >  1:185113/1‑76 (MQ=255)
                                                tttGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCaa                        <  1:4405199/76‑1 (MQ=255)
                                                  tGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATa                      >  2:2074886/1‑76 (MQ=255)
                                                  tGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATa                      >  2:6076903/1‑76 (MQ=255)
                                                  tGCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATa                      >  1:3328713/1‑76 (MQ=255)
                                                   gCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACCCTCCCGAATCATCAATaa                     <  1:4604735/76‑1 (MQ=255)
                                                   gCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATaa                     >  2:5718348/1‑76 (MQ=255)
                                                   gCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATaa                     <  2:984791/76‑1 (MQ=255)
                                                   gCTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATaa                     <  1:4124400/76‑1 (MQ=255)
                                                    cTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATaaa                    <  2:783467/76‑1 (MQ=255)
                                                    cTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATaaa                    >  2:6262763/1‑76 (MQ=255)
                                                    cTTTTGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATaaa                    <  1:1467805/76‑1 (MQ=255)
                                                     ttttGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAAc                   <  1:1115214/76‑1 (MQ=255)
                                                     ttttGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAAc                   >  2:6285156/1‑76 (MQ=255)
                                                     ttttGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAAc                   >  1:2670569/1‑76 (MQ=255)
                                                      tttGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACa                  >  2:4442181/1‑76 (MQ=255)
                                                       ttGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACAt                 <  1:2266742/76‑1 (MQ=255)
                                                       ttGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACAt                 <  1:36937/76‑1 (MQ=255)
                                                       ttGGATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACAt                 <  1:3592520/76‑1 (MQ=255)
                                                         ggATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATcc               >  1:4517301/1‑76 (MQ=255)
                                                          gATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATccc              <  1:5058357/76‑1 (MQ=255)
                                                          gATCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATccc              >  1:3675771/1‑76 (MQ=255)
                                                           aTCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATcccc             >  1:1600457/1‑76 (MQ=255)
                                                           aTCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATcccc             <  2:2909249/76‑1 (MQ=255)
                                                            tCTTTATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATccccc            <  1:5545563/76‑1 (MQ=255)
                                                               ttATATAAAATAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGtt         <  2:1291168/76‑1 (MQ=255)
                                                               ttATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGtt         >  1:1760032/1‑76 (MQ=255)
                                                               ttATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGtt         >  1:2458617/1‑76 (MQ=255)
                                                               ttATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGtt         <  2:430612/76‑1 (MQ=255)
                                                               ttATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGtt         <  2:400870/76‑1 (MQ=255)
                                                               ttATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGtt         >  1:4183911/1‑76 (MQ=255)
                                                               ttATATAAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGtt         >  1:4186645/1‑76 (MQ=255)
                                                                tatataAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTa        >  1:5587262/1‑76 (MQ=255)
                                                                tatataAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTa        >  1:4776114/1‑76 (MQ=255)
                                                                 atataAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTaa       <  2:4857814/76‑1 (MQ=255)
                                                                 atataAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTaa       >  1:1170768/1‑76 (MQ=255)
                                                                 atataAAACAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTaa       <  1:4601698/76‑1 (MQ=255)
                                                                   ataaaacaaaCTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACa     >  1:2453282/1‑76 (MQ=255)
                                                                   ataaaacaaaCTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACa     <  1:4204888/76‑1 (MQ=255)
                                                                   ataaaacaaaCTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACa     <  1:1210973/76‑1 (MQ=255)
                                                                    taaaacaaaCTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACaa    <  1:902291/76‑1 (MQ=255)
                                                                    taaaacaaaCTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACaa    >  1:3307564/1‑76 (MQ=255)
                                                                    taaaacaaaCTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACaa    >  1:1913541/1‑76 (MQ=255)
                                                                    taaaacaaaCTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACaa    <  2:4053754/76‑1 (MQ=255)
                                                                      aaacaaacTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACaaaa  <  2:5476288/76‑1 (MQ=255)
                                                                      aaacaaacTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACaaaa  <  2:1979126/76‑1 (MQ=255)
                                                                         |                                                                        
CCGAGTCCGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTTTATATAAAATAAACTTGGGAGCATAACGCCATCAGGTCTTAAACACTCCCGAATCATCAATAAACATCCCCCGTTAACAAAA  >  REL606/3011147‑3011292

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A