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 2,220,132 A→G 37.6% intergenic (+392/‑586) yhdH → / → accB predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding/acetyl CoA carboxylase, BCCP subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,220,1320AG37.6% 58.7 / 71.5 109intergenic (+392/‑586)yhdH/accBpredicted oxidoreductase, Zn‑dependent and NAD(P)‑binding/acetyl CoA carboxylase, BCCP subunit
Reads supporting (aligned to +/- strand):  ref base A (38/30);  new base G (21/20);  total (59/50)
Fisher's exact test for biased strand distribution p-value = 6.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 109 total aligned reads displayed.

ATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATC  >  minE/2220072‑2220199
                                                            |                                                                   
aTTTAATGCTGAGGATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGc                                                             <  1:641966/69‑1 (MQ=255)
   tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                           >  1:107086/1‑68 (MQ=255)
   tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                           >  1:686730/1‑68 (MQ=255)
   tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                           >  1:1250360/1‑68 (MQ=255)
   tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                           >  1:3190922/1‑68 (MQ=255)
   tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                           >  1:1379174/1‑68 (MQ=255)
        cTGAGCATTGTCAATCTGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaa                                                       <  1:2453476/67‑1 (MQ=255)
        cTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaaaa                                                     >  1:2311658/1‑69 (MQ=255)
        cTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaaaa                                                     >  1:2659609/1‑69 (MQ=255)
        cTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATCCAGTGaa                                                       <  1:2798390/67‑1 (MQ=255)
                 gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:1329202/1‑69 (MQ=255)
                 gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:2852399/1‑69 (MQ=255)
                 gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:3311580/1‑69 (MQ=255)
                 gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:3396810/1‑69 (MQ=255)
                 gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:3397861/1‑69 (MQ=255)
                 gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:3433526/1‑69 (MQ=255)
                 gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:1257900/1‑69 (MQ=255)
                 gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:398112/1‑69 (MQ=255)
                 gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:480035/1‑69 (MQ=255)
                 gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:728045/1‑69 (MQ=255)
                 gTCAATCGGTTAATTTTGAGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                            >  1:1933953/1‑69 (MQ=255)
                    aaTCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCATACGATGCAGTGaa                                                       <  1:2802793/55‑1 (MQ=255)
                    aaTCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaa                                                       <  1:966477/55‑1 (MQ=255)
                    aaTCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaa                                                       <  1:1118771/55‑1 (MQ=255)
                        ggTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGc                                     >  1:1792074/1‑69 (MQ=255)
                        ggTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGc                                     >  1:1823458/1‑69 (MQ=255)
                        ggTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGc                                     >  1:1382272/1‑69 (MQ=255)
                                   cGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaa                                                       <  1:2075797/40‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:1696831/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:672857/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:1178928/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:634487/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:125766/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:1083100/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:810475/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:3133097/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:3093408/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:1385690/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:2323723/68‑1 (MQ=255)
                                    gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                          <  1:2075920/68‑1 (MQ=255)
                                         ttAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtc                    <  1:1494461/69‑1 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:1546423/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:1978208/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:3087296/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:3044518/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:1666972/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:2713224/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:2670217/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:524976/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:567025/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:2450982/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:2166093/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:87845/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:1736179/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc                 >  1:673946/1‑68 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgt                  >  1:2192144/1‑67 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgt                  >  1:2262544/1‑67 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgt                  >  1:2801618/1‑67 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCt                >  1:2434730/1‑69 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCt                >  1:3228466/1‑69 (MQ=255)
                                             cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCt                >  1:3403391/1‑69 (MQ=255)
                                                 cacaTCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            >  1:1319983/1‑69 (MQ=255)
                                                 cacaTCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            >  1:2006799/1‑69 (MQ=255)
                                                 cacaTCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            >  1:24390/1‑69 (MQ=255)
                                                   caTCTTTCCGTACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:2814259/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:1306017/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:3344092/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:1367205/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:628599/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:1243142/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:1865242/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:5957/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:2151090/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:194611/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:199820/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:286960/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:2766524/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:2749602/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:2725639/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:3166103/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:219241/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:2491338/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:2037020/67‑1 (MQ=255)
                                                   caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt            <  1:2290816/67‑1 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGc                               >  1:1783804/1‑40 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTcgcg     <  1:174844/66‑1 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTcgcg     <  1:1729063/66‑1 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTcgcg     <  1:2234207/66‑1 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTcgcg     <  1:2651234/66‑1 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTcgcg     <  1:1486765/66‑1 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTcgcg     <  1:1392454/66‑1 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTcgc      >  1:1480204/1‑65 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTc        >  1:1033714/1‑63 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATc  >  1:629392/1‑69 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATc  >  1:1344520/1‑69 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATc  >  1:703531/1‑69 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATc  >  1:3160056/1‑69 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATc  >  1:1506615/1‑69 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATc  >  1:908691/1‑69 (MQ=255)
                                                           cAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTAGCGATc  >  1:3286197/1‑69 (MQ=255)
                                                            |                                                                   
ATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATC  >  minE/2220072‑2220199

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