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 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,933,624	T→A	13.3%	P273P (CCA→CCT)	lysS ←	lysine tRNA synthetase, constitutive

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,933,624	0	T	A	13.3%	296.0 / 30.8	112	P273P (CCA→CCT)	lysS	lysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand): ref base T (49/48); new base A (7/8); total (56/56)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 122 total aligned reads displayed.

GCGATTCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCAC  >  minE/1933554‑1933694

gCGATTCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAActct                                                                        <  1:3855310/71‑1 (MQ=255)

gCGATTCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAActct                                                                        <  1:2216259/71‑1 (MQ=255)

    ttCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAActct                                                                        <  1:1983370/67‑1 (MQ=255)

    atCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAActct                                                                        <  1:3503072/66‑1 (MQ=255)

      cGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTa                                                                  >  1:1169826/1‑71 (MQ=255)

      cGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTa                                                                  >  1:3364686/1‑71 (MQ=255)

         tCAGTTCAATCAAATCGTGGTAATCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTAt                                                                 <  1:607760/69‑1 (MQ=255)

         tCAGCTCAATCAAATCGTGGTAATCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATg                                                                <  1:2451787/70‑1 (MQ=255)

          cAGTTCAATCAAATCGTGGTAATCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTa                                                                  <  1:3128010/67‑1 (MQ=255)

          cAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGAc                                                              >  1:3286051/1‑71 (MQ=255)

            gCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACg                                                             >  1:1850673/1‑70 (MQ=255)

            gCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGt                                                            <  1:3595634/71‑1 (MQ=255)

            gCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGt                                                            <  1:3933959/71‑1 (MQ=255)

            gCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGt                                                            <  1:1877632/71‑1 (MQ=255)

                gATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACgg                                                        <  1:3446948/71‑1 (MQ=255)

                gATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACg                                                         >  1:3189364/1‑70 (MQ=255)

                gATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACg                                                         <  1:1206485/70‑1 (MQ=255)

                gATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACg                                                         >  1:3195083/1‑70 (MQ=255)

                gATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACg                                                         >  1:1757474/1‑70 (MQ=255)

                 aTCAGATCTTTGTAATCTGCGTAAGCCATGAAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGa                                                       <  1:1078116/71‑1 (MQ=255)

                  tCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGaa                                                      <  1:666948/71‑1 (MQ=255)

                  tCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGa                                                       >  1:3618664/1‑70 (MQ=255)

                   cAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTGCATCATGGTGAACTCTGGGTTATGACGTACGGaa                                                      <  1:1139601/70‑1 (MQ=255)

                      aTCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTggg                                                                     >  1:1431123/1‑52 (MQ=255)

                      aTCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTg                                                                       <  1:1558585/50‑1 (MQ=255)

                      aTCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGt                                                                    <  1:623521/53‑1 (MQ=255)

                      aTCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGa                                                       <  1:2270945/66‑1 (MQ=255)

                        cTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGaaa                                                     >  1:3423575/1‑66 (MQ=255)

                         tttGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGa                                                       <  1:2408485/63‑1 (MQ=255)

                          ttGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTc                                              >  1:3911701/1‑71 (MQ=255)

                          ttGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTc                                              >  1:3648812/1‑71 (MQ=255)

                          ttGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTc                                              >  1:3713919/1‑71 (MQ=255)

                           tGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCg                                             >  1:2566959/1‑71 (MQ=255)

                           tGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCg                                             >  1:3843048/1‑71 (MQ=255)

                               aTCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTAc                                         >  1:1800792/1‑71 (MQ=255)

                                tCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGt                                                                    <  1:3306925/43‑1 (MQ=255)

                                tCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGtt                                           <  1:1603635/68‑1 (MQ=255)

                                  tGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAAt                                                    >  1:2204062/1‑57 (MQ=255)

                                  tGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACgg                                       >  1:1432986/1‑70 (MQ=255)

                                    cGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACgg                                       <  1:3747255/68‑1 (MQ=255)

                                    cGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGaa                                     <  1:2727350/70‑1 (MQ=255)

                                    cGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAg                                    <  1:1151388/71‑1 (MQ=255)

                                      tAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACgg                                       >  1:1722944/1‑66 (MQ=255)

                                         gCCGTGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACg                               >  1:898899/1‑71 (MQ=255)

                                         gCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTa                                 <  1:3566231/69‑1 (MQ=255)

                                         gCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACg                               >  1:2009827/1‑71 (MQ=255)

                                          ccATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACgg                              <  1:31784/71‑1 (MQ=255)

                                          ccATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACgg                              <  1:3496383/71‑1 (MQ=255)

                                           cATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGt                             >  1:2432281/1‑71 (MQ=255)

                                           cATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGt                             <  1:606162/71‑1 (MQ=255)

                                            aTGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGa                                                       <  1:2149913/44‑1 (MQ=255)

                                            aTGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGtt                            <  1:3031687/71‑1 (MQ=255)

                                            aTGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGtt                            <  1:3346568/71‑1 (MQ=255)

                                             tGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGa                                                       <  1:1944385/43‑1 (MQ=255)

                                             tGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGt                             >  1:883771/1‑69 (MQ=255)

                                              gTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTAc                                <  1:272517/65‑1 (MQ=255)

                                               tAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGa                                                       <  1:3144676/41‑1 (MQ=255)

                                               tAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAt                         <  1:351408/71‑1 (MQ=255)

                                               tAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAt                         <  1:1258645/71‑1 (MQ=255)

                                                agagTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACTGAAGTTACGGTTGAtt                        >  1:2010645/1‑71 (MQ=255)

                                                agagTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAtt                        >  1:1596805/1‑71 (MQ=255)

                                                agagTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAtt                        >  1:3744116/1‑71 (MQ=255)

                                                 gagTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGAttt                       >  1:2922537/1‑71 (MQ=255)

                                                 gagTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAtt                        <  1:3868686/70‑1 (MQ=255)

                                                 gagTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAtt                        <  1:3854885/70‑1 (MQ=255)

                                                 gagTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAtt                        <  1:2123761/70‑1 (MQ=255)

                                                  agTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACgg                              <  1:2750015/63‑1 (MQ=255)

                                                  agTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACgg                              <  1:2640157/63‑1 (MQ=255)

                                                  agTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTc                      >  1:1255903/1‑71 (MQ=255)

                                                  agTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTc                      <  1:2960355/71‑1 (MQ=255)

                                                  agTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTc                      <  1:2596932/71‑1 (MQ=255)

                                                   gTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAt                         >  1:1976200/1‑67 (MQ=255)

                                                   gTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCg                     <  1:922304/71‑1 (MQ=255)

                                                   gTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCg                     <  1:2235807/71‑1 (MQ=255)

                                                    ttCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGtt                            >  1:3804349/1‑63 (MQ=255)

                                                    ttCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCg                     >  1:1794347/1‑70 (MQ=255)

                                                    ttCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCg                     >  1:3181857/1‑70 (MQ=255)

                                                     tCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGaa                   >  1:466830/1‑71 (MQ=255)

                                                      ccATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGaa                   <  1:3432322/70‑1 (MQ=255)

                                                        atcatTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTAccg                              >  1:1370776/1‑55 (MQ=255)

                                                        atcatGGTGAACTCTGGGTTATGACGTACGGAAATACCTTc                                              >  1:767046/1‑41 (MQ=255)

                                                        atcatGGTGAACTCTGGGTTATGACGTACGGAAATACCTTc                                              >  1:2138235/1‑41 (MQ=255)

                                                        atcatGGTGAACTCTGGGTTATGACGTACGGAAATACCTTc                                              >  1:1768892/1‑41 (MQ=255)

                                                         tcatGGTGAACTCTGGGTTATGACGTACGGAAATACCtt                                               <  1:3080424/39‑1 (MQ=255)

                                                          catTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATaccc              >  1:1453502/1‑69 (MQ=255)

                                                          catGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGaa                   >  1:442877/1‑66 (MQ=255)

                                                           atGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTa                                          >  1:2546357/1‑42 (MQ=255)

                                                            ttgTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCgt            <  1:2639753/69‑2 (MQ=255)

                                                              gTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTc          >  1:1442235/1‑71 (MQ=255)

                                                               tGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg         <  1:2740201/71‑1 (MQ=255)

                                                               tGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg         <  1:249991/71‑1 (MQ=255)

                                                               tGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg         <  1:3220104/71‑1 (MQ=255)

                                                                 aaCTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg         >  1:3250418/1‑69 (MQ=255)

                                                                 aaCTCAGGATTATGGCGAAGAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGaa                   >  1:1545477/1‑59 (MQ=255)

                                                                  aCTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCaaaa      <  1:3645128/71‑2 (MQ=255)

                                                                   ctctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc     >  1:3504748/1‑71 (MQ=255)

                                                                   ctctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc     >  1:3670150/1‑71 (MQ=255)

                                                                   ctctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc     <  1:843694/71‑1 (MQ=255)

                                                                   ctcaGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGa                    >  1:1400569/1‑56 (MQ=255)

                                                                     ctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcca   >  1:1724942/1‑71 (MQ=255)

GCGATTCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCAC  >  minE/1933554‑1933694

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