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 2,919,183 A→G 24.7% N171N (AAT→AAC)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,1830AG24.7% 179.4 / 60.6 105N171N (AAT→AAC) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base A (37/42);  new base G (13/13);  total (50/55)
Fisher's exact test for biased strand distribution p-value = 8.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.57e-01

Only 100 of 115 total aligned reads displayed.

GCCAGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAAT  >  minE/2919116‑2919253
                                                                   |                                                                      
gCCAGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTg                                                                     >  1:1937484/1‑71 (MQ=255)
     cACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAt                                                                >  1:4871008/1‑71 (MQ=255)
     cACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAt                                                                <  1:5379770/71‑1 (MQ=255)
      aCGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtg                                                               >  1:5530071/1‑71 (MQ=255)
      aCGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtg                                                               >  1:828795/1‑71 (MQ=255)
        gCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgtt                                                             <  1:2760971/71‑1 (MQ=255)
         cTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttg                                                            >  1:4587517/1‑71 (MQ=255)
         cTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttg                                                            <  1:5221718/71‑1 (MQ=255)
         cTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttg                                                            >  1:5289647/1‑71 (MQ=255)
         cTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttg                                                            >  1:2830975/1‑71 (MQ=255)
         cTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttg                                                            <  1:2172423/71‑1 (MQ=255)
          ttGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttgt                                                           >  1:1687036/1‑71 (MQ=255)
            gtgGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttgt                                                           <  1:3077901/69‑1 (MQ=255)
            gtgGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttgt                                                           <  1:119926/69‑1 (MQ=255)
            gtgGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttgt                                                           <  1:1535094/69‑1 (MQ=255)
            gtgGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAt                                                                >  1:3904542/1‑64 (MQ=255)
            gtgGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATgttgtt                                                          <  1:4070067/70‑1 (MQ=255)
            gtgGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTa                                                         >  1:4052399/1‑71 (MQ=255)
            gtgGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTa                                                         >  1:4634735/1‑71 (MQ=255)
             tgGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTa                                                         <  1:2505141/70‑1 (MQ=255)
               gcgcGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTAc                                                        >  1:4584176/1‑69 (MQ=255)
                cgcgACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGaa                                                                        >  1:2428705/1‑52 (MQ=255)
                cgcgACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGaa                                                                        >  1:755987/1‑52 (MQ=255)
                cgcgACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGaa                                                                        >  1:373128/1‑52 (MQ=255)
                    aacAGGCGCAGATCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATc                                                 <  1:5358180/69‑1 (MQ=255)
                     ccAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCa                                                >  1:2192899/1‑71 (MQ=255)
                     ccAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCa                                                <  1:4247850/71‑1 (MQ=255)
                     acAGGCGCAGATCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATgttgttg                                                         <  1:3921175/61‑2 (MQ=255)
                       aggcGCAGATCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGcc                                              >  1:145898/4‑71 (MQ=255)
                       aggcGCAGATCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGcc                                              >  1:4022555/4‑71 (MQ=255)
                           gCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAAtt                                                                      >  1:2304925/1‑43 (MQ=255)
                             agaTCCAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGcg                                          >  1:5596632/3‑68 (MQ=255)
                             aaaTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCa                                          >  1:1247361/1‑69 (MQ=255)
                                tCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGAc                                     >  1:5153413/1‑71 (MQ=255)
                                 ccAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATgttgttg                                                         >  1:3076390/1‑49 (MQ=25)
                                 ccAGCCCGGTCAGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGAc                                     >  1:4885901/1‑70 (MQ=255)
                                 ccAGACCGGTAAGCGCCGCAGCTTCGAGCATCGaa                                                                        >  1:1204862/1‑35 (MQ=255)
                                 ccAGACCGGTAAGCGCCGCAGCTTCGAGCATCGaa                                                                        >  1:1031895/1‑35 (MQ=255)
                                 ccAGACCGGTAAGCGCCGCAGCTTCGAGCATCGaa                                                                        >  1:2162195/1‑35 (MQ=255)
                                 ccAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgtt                                                             <  1:49549/46‑1 (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)
                                    gACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTAc                                                        <  1:4521722/48‑1 (MQ=255)
                                      ccGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttgt                                                           >  1:562637/1‑43 (MQ=255)
                                      ccGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCg                                <  1:4517453/70‑1 (MQ=255)
                                        ggTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCa                             <  1:1348139/71‑1 (MQ=255)
                                         gtcaGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGt                               <  1:1107373/65‑1 (MQ=255)
                                         gtcaGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGt                               <  1:2424723/65‑1 (MQ=255)
                                         gTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttgt                                                           <  1:148470/40‑1 (MQ=255)
                                         gTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAt                            >  1:3223895/1‑71 (MQ=255)
                                          tcaGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCAtc                           <  1:1755994/69‑2 (MQ=255)
                                          tcaGCGCCGCCGCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCAtc                           >  1:2944657/3‑70 (MQ=255)
                                          tAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTAcg                                                       <  1:3545084/43‑1 (MQ=255)
                                          tAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTAcg                                                       <  1:2150774/43‑1 (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)
                                                  gcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGaa                   <  1:4850436/71‑1 (MQ=255)
                                                      cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTc                                                 <  1:2764949/37‑1 (MQ=255)
                                                      cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTc                                                 <  1:1126282/37‑1 (MQ=255)
                                                      cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt               <  1:4436257/71‑1 (MQ=255)
                                                      cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt               <  1:5233290/71‑1 (MQ=255)
                                                      cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt               <  1:3143561/71‑1 (MQ=255)
                                                      cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt               <  1:3830421/71‑1 (MQ=255)
                                                      cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGGCAt                            <  1:3973324/58‑1 (MQ=255)
                                                         ccaGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTg            >  1:3993969/3‑71 (MQ=255)
                                                         cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTg            >  1:659017/1‑71 (MQ=255)
                                                         cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTg            >  1:3881427/1‑71 (MQ=255)
                                                          gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGc           >  1:4409404/1‑71 (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)
                                                              aTCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg       <  1:4243788/71‑1 (MQ=255)
                                                              aTCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg       <  1:5507909/71‑1 (MQ=255)
                                                               tCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCcgg       >  1:5584906/1‑70 (MQ=255)
                                                               tCGAATTGCCCGTGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCggg       >  1:4874228/1‑70 (MQ=255)
                                                               tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAg                                       <  1:4465935/38‑1 (MQ=255)
                                                               tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAg                                       <  1:510150/38‑1 (MQ=255)
                                                               tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAg                                       <  1:2038924/38‑1 (MQ=255)
                                                               tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt             <  1:921967/64‑1 (MQ=255)
                                                               tCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt             <  1:1921360/64‑1 (MQ=255)
                                                                cGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAttt                          >  1:4466983/1‑50 (MQ=255)
                                                                cGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAttt                          >  1:4026614/1‑50 (MQ=255)
                                                                 gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGaa                   >  1:2783816/1‑56 (MQ=255)
                                                                 gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGaa                   >  1:4053313/1‑56 (MQ=255)
                                                                 gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa     >  1:4089195/1‑70 (MQ=255)
                                                                 gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa     <  1:4625081/70‑1 (MQ=255)
                                                                   aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAAt  >  1:3432057/1‑71 (MQ=255)
                                                                   aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAAt  >  1:1202170/1‑71 (MQ=255)
                                                                   |                                                                      
GCCAGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAAT  >  minE/2919116‑2919253

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A