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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,887,935 C→A 37.1% L311L (CTG→CTT)  gudD ← (D)‑glucarate dehydratase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,887,9350CA37.1% 96.7 / 81.6 105L311L (CTG→CTT) gudD(D)‑glucarate dehydratase 1
Reads supporting (aligned to +/- strand):  ref base C (39/27);  new base A (12/27);  total (51/54)
Fisher's exact test for biased strand distribution p-value = 8.23e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.87e-01

Only 100 of 114 total aligned reads displayed.

TTCATGGCACATTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCATATT  >  minE/1887875‑1888003
                                                            |                                                                    
ttCATGGCACATTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGat                                                              >  1:3247214/1‑69 (MQ=255)
      gCACATTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCaa                                                         >  1:1507008/1‑68 (MQ=255)
      gCACATTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCaa                                                         >  1:2862298/1‑68 (MQ=255)
       cacaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACg                                                       >  1:1490118/1‑69 (MQ=255)
       cacaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACg                                                       >  1:10300/1‑69 (MQ=255)
       cacaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACg                                                       >  1:1457412/1‑69 (MQ=255)
       cacaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACg                                                       >  1:1283844/1‑69 (MQ=255)
       cacaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACg                                                       >  1:1222247/1‑69 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:2536934/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:218632/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:2160125/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:588231/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:2070480/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:2722505/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:1885151/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:1934038/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:1983077/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:2024260/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:1350759/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:2261900/69‑1 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATCGTCCAGAAATGCGGATCCGCAAGCGGGATATCAACgg                                                      >  1:1148730/1‑69 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATCGTCCAGAAATGCGGATCCGCAAGCGGGATATCAACgg                                                      >  1:2046989/1‑69 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATCGTCCAGAAATGCGGATCCGCAAGCGGGATATCAACgg                                                      >  1:42747/1‑69 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATCGTCCAGAAATGCGGATCCGCAAGCGGGATATCAACgg                                                      >  1:2698767/1‑69 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATCGTCCAGAAATGCGGATCCGCAAGCGGGATATCAACgg                                                      >  1:490845/1‑69 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATCGTCCAGAAATGCGGATCCGCAAGCGGGATATCAACgg                                                      >  1:1208729/1‑69 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATCGTCCAGAAATGCGGATCCGCAAGCGGGATATCAACgg                                                      >  1:1698942/1‑69 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATCGTCCAGAAATGCGGATCCGCAAGCGGGATATCAACgg                                                      >  1:3348935/1‑69 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATCGTCCAGAAATGCGGATCCGCAAGCGGGATATCAACgg                                                      >  1:2905838/1‑69 (MQ=255)
        acaTTTGCGCCACACGTACCGAACCTTGCATCGTCCAGAAATGCGGATCCGCAAGCGGGATATCAACgg                                                      >  1:755405/1‑69 (MQ=255)
             tGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGc                                                 >  1:3092619/1‑69 (MQ=255)
             tGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGc                                                 >  1:3383785/1‑69 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGATATGCGGATCCGCCAg                                                                    >  1:1079303/1‑41 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCTGGATATCAACGGa                                                     >  1:1861792/1‑56 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:2528698/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:565400/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:2393195/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:2760364/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:2578854/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:1777985/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:176296/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:160540/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:307499/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:839407/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:1143159/1‑68 (MQ=255)
                      cGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGagag                                         >  1:3216149/1‑68 (MQ=255)
                       gTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCg                                       <  1:246588/69‑1 (MQ=255)
                       gTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCg                                       <  1:867868/69‑1 (MQ=255)
                         agcGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACgg                                                      <  1:3230040/50‑1 (MQ=255)
                         aCCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTa                                     <  1:1546502/69‑1 (MQ=255)
                                       tGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTgcc                        >  1:3222960/1‑68 (MQ=255)
                                       tGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTgcc                        >  1:3040336/1‑68 (MQ=255)
                                       tGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTgcc                        >  1:2424221/1‑68 (MQ=255)
                                       tGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTgcc                        >  1:1918155/1‑68 (MQ=255)
                                       tGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTgcc                        >  1:1108124/1‑68 (MQ=255)
                                       tGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTgcc                        >  1:1562955/1‑68 (MQ=255)
                                       tGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTgcc                        >  1:698848/1‑68 (MQ=255)
                                       tGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTgcc                        >  1:1501800/1‑68 (MQ=255)
                                       tGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGG‑CCATTTgcc                        >  1:1347234/1‑67 (MQ=255)
                                       tGTCCAGAAATGCGGATCCGCCAGCGGGATATCAAAGGATTGCAGGGAGAGCGTATGGCCCATTTgcc                        >  1:2250498/1‑68 (MQ=255)
                                        gTCCAGAAATGCGGATCCGCCAGCGGGATATCAACg                                                       <  1:3261663/36‑1 (MQ=255)
                                           cAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAg                   >  1:221364/1‑69 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCTACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:2078504/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCATTCGGTg             <  1:6967/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:2388054/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:913751/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:860401/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:761242/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:3253871/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:688476/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:662518/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:582516/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:1046581/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:1047590/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:3150522/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:2802384/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:2465786/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:1532014/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:1001135/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:1743488/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:1882652/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:193865/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:2131451/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:2116415/69‑1 (MQ=255)
                                                 tGCGGATCCGCAAGCGGGATATCAACGGATTGCAACGAGAGCGTATGGCCCATCTGCCGCCAGTCGGTg             <  1:2037082/69‑1 (MQ=255)
                                                      aTCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGAt        <  1:767663/69‑1 (MQ=255)
                                                        ccGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCa      <  1:1016165/69‑1 (MQ=255)
                                                        ccGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCa      <  1:1324418/69‑1 (MQ=255)
                                                        ccGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCa      <  1:2232777/69‑1 (MQ=255)
                                                        ccGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCa      <  1:3329995/69‑1 (MQ=255)
                                                        ccGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCa      <  1:3234866/69‑1 (MQ=255)
                                                         cGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCa      <  1:3238789/68‑1 (MQ=255)
                                                            cAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCATAtt  <  1:231796/69‑1 (MQ=255)
                                                            cAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCATAtt  <  1:413907/69‑1 (MQ=255)
                                                            cAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCATAtt  <  1:3352354/69‑1 (MQ=255)
                                                            cAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCATAtt  <  1:1530434/69‑1 (MQ=255)
                                                            cAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCATAtt  <  1:1403620/69‑1 (MQ=255)
                                                            cAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCATAtt  <  1:800762/69‑1 (MQ=255)
                                                            cAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCATAtt  <  1:2806998/69‑1 (MQ=255)
                                                            cAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCATAtt  <  1:3217921/69‑1 (MQ=255)
                                                            |                                                                    
TTCATGGCACATTTGCGCCACACGTACCGAACCTTGCATTGTCCAGAAATGCGGATCCGCCAGCGGGATATCAACGGATTGCAGGGAGAGCGTATGGCCCATTTGCCGCCAGTCGGTGGCGATCATATT  >  minE/1887875‑1888003

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