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 2,919,204 G→A 27.9% D164D (GAC→GAT)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,2040GA27.9% 185.5 / 78.1 118D164D (GAC→GAT) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base G (33/52);  new base A (18/15);  total (51/67)
Fisher's exact test for biased strand distribution p-value = 1.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 124 total aligned reads displayed.

ACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGAT  >  minE/2919136‑2919274
                                                                    |                                                                      
aacAGGCGCAGATCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATc                                                                      <  1:5358180/69‑1 (MQ=255)
 ccAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCa                                                                     <  1:4247850/71‑1 (MQ=255)
 ccAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCa                                                                     >  1:2192899/1‑71 (MQ=255)
   aggcGCAGATCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGcc                                                                   >  1:145898/4‑71 (MQ=255)
   aggcGCAGATCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGcc                                                                   >  1:4022555/4‑71 (MQ=255)
         agaTCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGcg                                                               >  1:5596632/3‑68 (MQ=255)
         aaaTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCa                                                               >  1:1247361/1‑69 (MQ=255)
            tCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGAc                                                          >  1:5153413/1‑71 (MQ=255)
             ccAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGAc                                                          >  1:4885901/1‑70 (MQ=255)
              cAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGAcc                                                         <  1:445215/70‑1 (MQ=255)
              cAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCa                                                        <  1:4257598/71‑1 (MQ=255)
              cAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCa                                                        <  1:4250852/71‑1 (MQ=255)
               aGACCGGTAAGCGCCGCAGCTTCGAGGATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAg                                                            <  1:2021795/66‑1 (MQ=255)
               aGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAg                                                       >  1:2108848/1‑71 (MQ=255)
                  ccGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCg                                                     <  1:4517453/70‑1 (MQ=255)
                     gtcaGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGt                                                    <  1:1107373/65‑1 (MQ=255)
                     gTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAt                                                 >  1:3223895/1‑71 (MQ=255)
                      tcaGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCAtc                                                <  1:1755994/69‑2 (MQ=255)
                      tcaGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCAtc                                                >  1:2944657/3‑70 (MQ=255)
                        aGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCAtctc                                              <  1:792831/71‑1 (MQ=255)
                        aGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                                              >  1:813929/1‑71 (MQ=255)
                        aGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                                              >  1:826624/1‑71 (MQ=255)
                           gccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                                              <  1:851775/68‑1 (MQ=255)
                           gccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGtt                                           >  1:1749934/1‑71 (MQ=255)
                            ccgccgCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATc                                                                      >  1:4913882/1‑43 (MQ=19)
                            ccgccgCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATc                                                                      >  1:849816/1‑43 (MQ=19)
                            ccgccgCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGtta                                          <  1:4529423/71‑2 (MQ=255)
                             cgccgcTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGtta                                          <  1:2074957/70‑2 (MQ=255)
                                  cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTc                                                                      <  1:1126282/37‑1 (MQ=255)
                                  cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTc                                                                      <  1:2764949/37‑1 (MQ=255)
                                  cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                    <  1:4436257/71‑1 (MQ=255)
                                  cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                    <  1:3830421/71‑1 (MQ=255)
                                  cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                    <  1:5233290/71‑1 (MQ=255)
                                  cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGGCAt                                                 <  1:3973324/58‑1 (MQ=255)
                                     ccaGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTg                                 >  1:3993969/3‑71 (MQ=255)
                                     cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTg                                 >  1:659017/1‑71 (MQ=255)
                                      gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGc                                >  1:3463588/1‑71 (MQ=255)
                                      gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGc                                >  1:2560428/1‑71 (MQ=255)
                                      gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACAAGCGTCATTTCGTTGAACGATTTGc                                >  1:2598751/1‑71 (MQ=255)
                                      caGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTga                                >  1:3453267/2‑70 (MQ=255)
                                       aGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGtta                                          <  1:20650/60‑2 (MQ=255)
                                       aGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGc                                <  1:3308479/70‑1 (MQ=255)
                                       aGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc                               <  1:3209364/71‑1 (MQ=255)
                                        gCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGcg                                                               <  1:3255058/38‑2 (MQ=16)
                                          aTCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                            <  1:5507909/71‑1 (MQ=255)
                                           tCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCa                                                        >  1:5395084/1‑42 (MQ=16)
                                           tCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                            >  1:5584906/1‑70 (MQ=255)
                                           tCGAATTGCCCGTGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCggg                            >  1:4874228/1‑70 (MQ=255)
                                           tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAg                                                            <  1:510150/38‑1 (MQ=255)
                                           tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAg                                                            <  1:2038924/38‑1 (MQ=255)
                                           tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAg                                                            <  1:4465935/38‑1 (MQ=255)
                                           tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                  <  1:4486841/64‑1 (MQ=255)
                                           tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                  <  1:921967/64‑1 (MQ=255)
                                           tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                  <  1:1921360/64‑1 (MQ=255)
                                            cGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAttt                                               >  1:4466983/1‑50 (MQ=255)
                                             gagttGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                            >  1:2192853/4‑68 (MQ=255)
                                             gagttGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                            >  1:1837444/4‑68 (MQ=255)
                                             gagttGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg                            >  1:4565363/4‑68 (MQ=255)
                                             gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGaa                                        >  1:4053313/1‑56 (MQ=255)
                                             gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGaa                                        >  1:4046558/1‑56 (MQ=255)
                                             gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                          <  1:4625081/70‑1 (MQ=255)
                                             gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                          >  1:4089195/1‑70 (MQ=255)
                                              aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                          <  1:1329905/53‑1 (MQ=255)
                                               aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAAt                       >  1:3432057/1‑71 (MQ=255)
                                               aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAAt                       >  1:1202170/1‑71 (MQ=255)
                                                ttGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGtt                                           <  1:3869899/50‑1 (MQ=255)
                                                ttGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGtt                                           <  1:1552780/50‑1 (MQ=255)
                                                 tGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGc                     >  1:663767/1‑71 (MQ=255)
                                                  gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGc                     <  1:181489/70‑1 (MQ=255)
                                                  gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGc                     <  1:3273038/70‑1 (MQ=255)
                                                   cccATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                   <  1:5137429/71‑1 (MQ=255)
                                                    ccATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTc                                                   <  1:691142/38‑1 (MQ=16)
                                                    ccATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTc                                                   <  1:1916129/38‑1 (MQ=16)
                                                     cATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTc                                                   <  1:1559139/37‑1 (MQ=16)
                                                      aTGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCgg                             <  1:760622/58‑1 (MQ=255)
                                                      aTGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCgg                             <  1:4587879/58‑1 (MQ=255)
                                                       tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                                              <  1:4227771/40‑1 (MQ=255)
                                                       tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                          <  1:708782/44‑1 (MQ=255)
                                                       tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc                               <  1:2221004/55‑1 (MQ=255)
                                                       tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                   <  1:5407096/67‑1 (MQ=255)
                                                       tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTg                >  1:4613013/1‑70 (MQ=255)
                                                       tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGc               <  1:2808378/71‑1 (MQ=255)
                                                        gttgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGa                                         <  1:2684960/44‑1 (MQ=255)
                                                         ttgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                   >  1:4593094/1‑65 (MQ=255)
                                                         ttgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                   >  1:1514884/1‑65 (MQ=255)
                                                         ttgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCa              <  1:5141844/70‑1 (MQ=255)
                                                          tgttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATg            >  1:2632796/1‑71 (MQ=255)
                                                          tgttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATg            >  1:911300/1‑71 (MQ=255)
                                                          tgttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATg            >  1:3016110/1‑71 (MQ=255)
                                                          tgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCgg                             <  1:373920/54‑1 (MQ=255)
                                                          tgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCgg                             >  1:2894917/1‑54 (MQ=255)
                                                           gttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCt                    >  1:647392/1‑62 (MQ=255)
                                                            ttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATTGt          <  1:2013748/71‑1 (MQ=255)
                                                             tACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATg            >  1:2044921/1‑68 (MQ=255)
                                                             tACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATg            >  1:4202588/1‑68 (MQ=255)
                                                             tACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGt          >  1:3598803/1‑70 (MQ=255)
                                                                gcgcgTCACGTGCATAGACCAGCGTCATTTCGTTGTACGCt                                    <  1:3950997/41‑1 (MQ=38)
                                                                 cgcaTCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGc               <  1:4367059/61‑1 (MQ=255)
                                                                    gTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTgag       >  1:5313960/1‑66 (MQ=255)
                                                                    gTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGAt  <  1:4850782/71‑1 (MQ=255)
                                                                    |                                                                      
ACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGAT  >  minE/2919136‑2919274

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