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 2,555,880 C→T 53.6% A112A (GCG→GCA)  gpmI ← phosphoglycero mutase III, cofactor‑independent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,555,8800CT53.6% 15.1 / 121.3 138A112A (GCG→GCA) gpmIphosphoglycero mutase III, cofactor‑independent
Reads supporting (aligned to +/- strand):  ref base C (54/10);  new base T (14/60);  total (68/70)
Fisher's exact test for biased strand distribution p-value = 5.34e-15
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 138 total aligned reads displayed.

ATCGCCATGATGTGATCTTCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCAAAGAAAGCGCG  >  minE/2555815‑2555945
                                                                 |                                                                 
aTCGCCATGATGTGATCTTCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCt                                                                >  1:2474193/1‑69 (MQ=255)
aTCGCCATGATGTGATCTTCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCt                                                                >  1:1601251/1‑69 (MQ=255)
aTCGCCATGATGTGATCTTCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCt                                                                >  1:822425/1‑69 (MQ=255)
aTCGCCATGATGTGATCTTCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCt                                                                >  1:912633/1‑69 (MQ=255)
aTCGCCATGATGTGATCTTCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCt                                                                >  1:2557456/1‑69 (MQ=255)
aTCGCCATGATGTGATCTTCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCt                                                                >  1:2269024/1‑69 (MQ=255)
   gCCATGATGTGATCTTCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTg                                                             >  1:3425106/1‑69 (MQ=255)
         atgTGATCTTCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCg                                                       >  1:75220/1‑69 (MQ=255)
         atgTGATCTTCGTGGCTGTGTACACCACCTGCGGAGAGCATACCCATAATGTGTACTGCttt                                                              <  1:3203661/62‑1 (MQ=255)
         atgTGATCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCttt                                                              <  1:1033131/62‑1 (MQ=255)
         atgTGATCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCttt                                                              <  1:1208095/62‑1 (MQ=255)
         atgTGATCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCttt                                                              <  1:37967/62‑1 (MQ=255)
         atgTGATCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCttt                                                              <  1:1057093/62‑1 (MQ=255)
         atgTGATCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCttt                                                              <  1:1479397/62‑1 (MQ=255)
         atgTGATCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCttt                                                              <  1:2333540/62‑1 (MQ=255)
         atgTGATCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCttt                                                              <  1:1488432/62‑1 (MQ=255)
         atgTGATCATCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCg                                                       >  1:1836677/1‑69 (MQ=255)
               tCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTc                                                 >  1:2326685/1‑69 (MQ=255)
               tCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTc                                                 >  1:835176/1‑69 (MQ=255)
               tCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTc                                                 >  1:507142/1‑69 (MQ=255)
               tCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTc                                                 >  1:1918919/1‑69 (MQ=255)
               tCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTc                                                 >  1:2893992/1‑69 (MQ=255)
               tCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTc                                                 >  1:2941956/1‑69 (MQ=255)
               tCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTc                                                 >  1:3395778/1‑69 (MQ=255)
               tCTTCGTGGCTGTGTACACCACCTGCGGAGAGCAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTc                                                 >  1:1237611/1‑69 (MQ=255)
                 ttCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGc                                               >  1:1714229/1‑69 (MQ=255)
                     tGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGc                                               <  1:1616458/65‑1 (MQ=255)
                     tGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGc                                               <  1:1221931/65‑1 (MQ=255)
                     tGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGc                                               <  1:668923/65‑1 (MQ=255)
                     tGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGc                                               <  1:2005982/65‑1 (MQ=255)
                     tGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGc                                               <  1:2490204/65‑1 (MQ=255)
                     tGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGc                                               <  1:1317605/65‑1 (MQ=255)
                             tACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGttt                                                    >  1:2128197/1‑52 (MQ=255)
                             tACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACcgc                                   >  1:1188843/1‑69 (MQ=255)
                             tACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACcgc                                   >  1:3259122/1‑69 (MQ=255)
                             tACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACcgc                                   >  1:682528/1‑69 (MQ=255)
                             tACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACcgc                                   >  1:177931/1‑69 (MQ=255)
                             tACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACcgc                                   >  1:444996/1‑69 (MQ=255)
                             tACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACcgc                                   >  1:2904147/1‑69 (MQ=255)
                               cgccgcCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTAt                                          >  1:1569668/1‑60 (MQ=255)
                               cgccgcCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACcgc                                   >  1:3147040/1‑67 (MQ=255)
                               cgccgcCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACcg                                    >  1:438403/1‑66 (MQ=255)
                                            gagCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCgg                    <  1:2034900/69‑1 (MQ=255)
                                            gagCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCgg                    <  1:2478305/69‑1 (MQ=255)
                                               cAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGAtt                 <  1:1204725/69‑1 (MQ=255)
                                               cAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGAtt                 <  1:2881997/69‑1 (MQ=255)
                                               cAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGAtt                 <  1:3203421/69‑1 (MQ=255)
                                               cAGACCCATAATGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGAtt                 <  1:1647969/69‑1 (MQ=255)
                                                 gACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTa                >  1:2664335/1‑68 (MQ=255)
                                                   cccATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAg               >  1:2842639/1‑67 (MQ=255)
                                                   cccATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAg               >  1:783604/1‑67 (MQ=255)
                                                   cccATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAg               >  1:690887/1‑67 (MQ=255)
                                                   cccATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAg               >  1:2886792/1‑67 (MQ=255)
                                                   cccATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATATACCGCGCAAGTCAGCACCGGATTAg               >  1:445557/1‑67 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTATCaaaga         <  1:1372314/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:1994598/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:1408036/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:2444727/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:3168373/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:500016/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:1560707/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:190280/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:1297029/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:2075479/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:3224939/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:3235367/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:2137951/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:2255354/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:1231742/67‑1 (MQ=255)
                                                         aTGTGTACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCaaaga         <  1:1069560/67‑1 (MQ=255)
                                                         aTGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAg                              >  1:3024574/1‑46 (MQ=255)
                                                         aTGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCaaagaaa       >  1:191020/1‑69 (MQ=255)
                                                         aTGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCaaagaaa       >  1:2743469/1‑69 (MQ=255)
                                                         aTGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCaaagaaa       >  1:211596/1‑69 (MQ=255)
                                                         aTGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCaaagaaa       >  1:512871/1‑69 (MQ=255)
                                                         aTGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCaaagaaa       >  1:1039693/1‑69 (MQ=255)
                                                         aTGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCaaagaaa       >  1:464660/1‑69 (MQ=255)
                                                         aTGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCaaagaaa       >  1:2256595/1‑69 (MQ=255)
                                                         aTGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCaaagaa        >  1:1487678/1‑68 (MQ=255)
                                                           gtgtACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGAtt                 <  1:1052270/57‑1 (MQ=255)
                                                            tgtACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGc                         >  1:1195758/1‑48 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgctc   <  1:3117798/68‑3 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:991614/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:470184/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:993177/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:2945740/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:2707706/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:2526846/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:2451920/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:2375022/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:2182014/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:2118593/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:2039419/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:1814148/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:1704065/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:1370707/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:1204703/68‑1 (MQ=255)
                                                              tACTGCTTTGCCTGCGTTTTTCGCTTTATCTACTGCACCAGTCAACACCGGATTAGCAAAGAAAgcgc   <  1:1099489/68‑1 (MQ=255)
                                                              tACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCAAAGAAAgcgc   >  1:3354249/1‑68 (MQ=255)
                                                              tACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCAAAGAAAGcgcg  >  1:340675/1‑69 (MQ=255)
                                                                 |                                                                 
ATCGCCATGATGTGATCTTCGTGGCTGTGTACGCCGCCTGCGGAGAGCAGACCCATAATGTGTACCGCTTTGCCTGCGTTTTTCGCTTTATCTACCGCGCCAGTCAGCACCGGATTAGCAAAGAAAGCGCG  >  minE/2555815‑2555945

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