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 1,837,447 A→C 25.2% S324R (AGT→AGG) ‡ nlpD ← predicted outer membrane lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,837,4470AC25.2% 149.7 / 82.3 115S324R (AGT→AGG) ‡nlpDpredicted outer membrane lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (43/43);  new base C (17/12);  total (60/55)
Fisher's exact test for biased strand distribution p-value = 5.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

Only 100 of 117 total aligned reads displayed.

ATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATA  >  minE/1837382‑1837515
                                                                 |                                                                    
aTTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAg                                                                 >  1:593596/1‑71 (MQ=255)
 ttttttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCa                                                                      >  1:951753/1‑65 (MQ=255)
 ttttttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCa                                                                      >  1:2703336/1‑65 (MQ=255)
 ttttttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAgg                                                                >  1:935329/1‑71 (MQ=255)
 ttttttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAgg                                                                >  1:2161948/1‑71 (MQ=255)
   ttttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGt                                                               >  1:3680270/1‑70 (MQ=255)
   ttttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGt                                                               >  1:725762/1‑70 (MQ=255)
    tttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTa                                                              <  1:1873702/70‑1 (MQ=255)
     ttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTaa                                                             <  1:3033293/70‑1 (MQ=255)
          ccGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAatcat                                                         <  1:2586968/69‑1 (MQ=255)
           cGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAAtcatca                                                       >  1:2363276/1‑70 (MQ=255)
           cGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATcatcat                                                      >  1:3523343/1‑71 (MQ=255)
           cGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATcatcat                                                      >  1:1830435/1‑71 (MQ=255)
            gCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATcatcat                                                      >  1:1943963/1‑70 (MQ=255)
            gCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATcatcat                                                      >  1:4166284/1‑70 (MQ=255)
             ccTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTa                                                    >  1:1506986/1‑71 (MQ=255)
              cTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTAt                                                   >  1:3004534/1‑71 (MQ=255)
               ttAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAatcat                                                         <  1:3249820/64‑1 (MQ=255)
                 aaCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTa                                                              >  1:5319443/1‑57 (MQ=255)
                 aaCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTa                                                              >  1:2614351/1‑57 (MQ=255)
                 aaCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt                                                 >  1:3185901/1‑70 (MQ=255)
                  aCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt                                               <  1:5127570/71‑1 (MQ=255)
                  aCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt                                               <  1:2222326/71‑1 (MQ=255)
                  aCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt                                               <  1:3627885/71‑1 (MQ=255)
                  aCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt                                               <  1:5594504/71‑1 (MQ=255)
                   cttcttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGtt                                                <  1:254132/69‑1 (MQ=255)
                   cttcttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGtt                                                <  1:3885381/69‑1 (MQ=255)
                       ttgttgTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTa                                                              <  1:4508513/51‑1 (MQ=255)
                        tgttgtTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgatga                                          >  1:3877715/1‑70 (MQ=255)
                         gttgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgatga                                          <  1:4754187/69‑1 (MQ=255)
                         gttgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgatga                                          <  1:5424680/69‑1 (MQ=255)
                         gttgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTgatgat                                         <  1:4205122/70‑1 (MQ=255)
                            gttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgat                                            >  1:3393886/1‑64 (MQ=255)
                             ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATc                                     <  1:470958/70‑1 (MQ=255)
                             ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATc                                     <  1:1129091/70‑1 (MQ=255)
                             ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa                                    <  1:4905618/71‑1 (MQ=255)
                               cccGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCa                                                                  >  1:1274032/1‑39 (MQ=255)
                               cccGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGtt                                                >  1:2303730/1‑57 (MQ=255)
                                 tttaCCAGCATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGAt                                 <  1:940574/67‑1 (MQ=255)
                                 tttaCCAGCATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGAt                                 <  1:216349/67‑1 (MQ=255)
                                 cGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGAtt                                <  1:2104168/71‑1 (MQ=255)
                                      cAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTAt                                                   <  1:918072/47‑1 (MQ=255)
                                      cAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGt                           <  1:210467/71‑1 (MQ=255)
                                       aGCATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGt                           <  1:2273518/70‑1 (MQ=255)
                                        gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt                                                 >  1:1609507/1‑47 (MQ=255)
                                        gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt                                                 >  1:4418962/1‑47 (MQ=255)
                                        gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt                                                 >  1:4194240/1‑47 (MQ=255)
                                        gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt                                                 >  1:3298963/1‑47 (MQ=255)
                                        gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTgatgat                                         <  1:5178212/55‑1 (MQ=255)
                                        gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTgatgat                                         <  1:760127/55‑1 (MQ=255)
                                        gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTgatgat                                         <  1:3767932/55‑1 (MQ=255)
                                        gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAg                         <  1:969777/71‑1 (MQ=255)
                                        gCATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAg                         >  1:4278880/1‑71 (MQ=255)
                                         cATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGc                        <  1:169398/71‑1 (MQ=255)
                                         cATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGc                        >  1:5110646/1‑71 (MQ=255)
                                          atcgtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGc                        >  1:2584178/4‑70 (MQ=255)
                                           ttGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTa                                                    <  1:398584/41‑1 (MQ=255)
                                           ttGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgat                                            >  1:1587023/1‑49 (MQ=255)
                                           ttGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCg                            >  1:2007803/1‑65 (MQ=255)
                                           ttGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAg                         >  1:1663468/1‑68 (MQ=255)
                                           ttGTGTAGTTATGGGCGTAGGCACTCAGGTAATCATCATTa                                                    <  1:503388/41‑1 (MQ=255)
                                            tgtgTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCcgc                     >  1:4724543/1‑71 (MQ=255)
                                            tgtgTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCcg                      >  1:4044360/1‑70 (MQ=255)
                                             gtgtCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCcgcg                    >  1:1290134/1‑71 (MQ=255)
                                             gtgtCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCcgcg                    >  1:3937281/1‑71 (MQ=255)
                                             gtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGccac                     <  1:3115612/70‑3 (MQ=255)
                                             gtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCcacg                    >  1:2447017/1‑71 (MQ=255)
                                             gtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCcacg                    >  1:3550347/1‑71 (MQ=255)
                                             gtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCcacg                    >  1:865233/1‑71 (MQ=255)
                                             gtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACAGTAGCcacg                    >  1:5366931/1‑71 (MQ=255)
                                              tgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATgaga                                  >  1:3683978/1‑56 (MQ=255)
                                              tgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATgaga                                  >  1:744114/1‑56 (MQ=255)
                                                tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAg                         >  1:832223/4‑63 (MQ=255)
                                                tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCa                  <  1:4151842/67‑1 (MQ=255)
                                                tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCa                  <  1:147037/67‑1 (MQ=255)
                                                tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAg                 >  1:4552884/4‑71 (MQ=255)
                                                tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAg                 >  1:435145/4‑71 (MQ=255)
                                                tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtga                                             >  1:5143050/1‑43 (MQ=255)
                                                tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAg                                   <  1:5070809/53‑1 (MQ=255)
                                                 cattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTAcc                             >  1:1162839/3‑58 (MQ=255)
                                                 cattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAg                 >  1:5488917/3‑70 (MQ=255)
                                                  gTTATGGGCGTAGGCACTCAGGTAATCATCATTAt                                                   <  1:2391443/35‑1 (MQ=255)
                                                  gTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAgcg               >  1:279509/1‑71 (MQ=255)
                                                  gTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAga                >  1:2485721/1‑69 (MQ=255)
                                                  attATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGAt                                 >  1:2727593/2‑53 (MQ=255)
                                                  attATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTAcc                             >  1:3314409/2‑57 (MQ=255)
                                                  attATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGccac                     <  1:2958374/64‑3 (MQ=255)
                                                  attATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgct               <  1:4579251/70‑2 (MQ=255)
                                                   ttATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgctg              <  1:5610259/71‑3 (MQ=255)
                                                   ttATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgctg              <  1:2302439/71‑3 (MQ=255)
                                                   ttATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgctg              <  1:4749363/71‑3 (MQ=255)
                                                   taaTGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCa                  <  1:1184967/65‑1 (MQ=255)
                                                    tATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAgcgc              >  1:4100491/1‑70 (MQ=255)
                                                      tGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGtt           <  1:2870711/71‑1 (MQ=255)
                                                       gggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATaa                                       >  1:3229625/1‑42 (MQ=255)
                                                       gggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAAt                                      >  1:4294273/1‑43 (MQ=255)
                                                       gggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAAt                                      >  1:4626672/1‑43 (MQ=255)
                                                         gCGTAGGCACTCAGGTAATCATCATTATGTTTgatgat                                         <  1:1852372/38‑1 (MQ=255)
                                                            tAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa                                    <  1:1068833/40‑1 (MQ=255)
                                                               gCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATa  <  1:1831448/71‑1 (MQ=255)
                                                                 |                                                                    
ATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATA  >  minE/1837382‑1837515

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