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	1,933,651	G→A	21.4%	N264N (AAC→AAT)	lysS ←	lysine tRNA synthetase, constitutive

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,933,651	0	G	A	21.4%	200.8 / 48.4	98	N264N (AAC→AAT)	lysS	lysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand): ref base G (40/37); new base A (13/8); total (53/45)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01

TGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGT  >  minE/1933581‑1933720

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

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

  tAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGtt                                                                     <  1:3654142/71‑1 (MQ=255)

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

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

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

         cGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACgg                                                                 <  1:3763661/68‑1 (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)

             aGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTa                                                           <  1:3129073/70‑1 (MQ=255)

             aGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTa                                                           <  1:2531258/70‑1 (MQ=255)

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

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

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

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

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

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

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

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

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

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

                   gTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTAc                                                          <  1:272517/65‑1 (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                                                  <  1:3854885/70‑1 (MQ=255)

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

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

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

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

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

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

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

                        gTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTc                                                >  1:1558291/1‑70 (MQ=255)

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

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

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

                        gTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCg                                               <  1:3881830/71‑1 (MQ=255)

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

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

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

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

                           ccATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTAc                                                                   >  1:92746/1‑48 (MQ=255)

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

                             atcatTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTAccg                                                        >  1:1370776/1‑55 (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)

                                 tGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGtt                                                      >  1:1989752/1‑55 (MQ=255)

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

                                    tGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGaa                                             >  1:3324809/1‑61 (MQ=255)

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

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

                                    tGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg                                   <  1:249991/71‑1 (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)

                                           tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccac                            >  1:3473895/1‑71 (MQ=255)

                                              attATGGCGAACAGAAATACCTTCATTACGGAAGtt                                                            <  1:1261407/35‑1 (MQ=16)

                                               ttATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCgcctac                        <  1:922462/71‑1 (MQ=255)

                                               ttATGACGTACGGAAATACCTTCGTTAGGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCaccaac                        <  1:1063126/71‑1 (MQ=255)

                                                tATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGa                                              >  1:374608/1‑48 (MQ=37)

                                                tATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGaa                                             <  1:989539/49‑1 (MQ=255)

                                                tATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATac                                          >  1:2349790/1‑52 (MQ=255)

                                                  tGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAaccac                     <  1:1300805/71‑1 (MQ=255)

                                                   gACGTACGGATATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGaa                                 >  1:1274816/1‑58 (MQ=255)

                                                   gACGTACGGATATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGaa                                 >  1:1279412/1‑58 (MQ=255)

                                                   gACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAtt                                                  >  1:782713/1‑41 (MQ=255)

                                                    aCGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAaccacc                    <  1:3086059/70‑1 (MQ=255)

                                                     cGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAaccac                     >  1:3630647/1‑68 (MQ=255)

                                                     cGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAaccac                     >  1:1376230/1‑68 (MQ=255)

                                                      gTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcca                             >  1:189450/1‑59 (MQ=255)

                                                       tACGGAAATACCTTCGTTACGGAAGTTACGGTTGAtt                                                  >  1:3913098/1‑37 (MQ=255)

                                                       tACGGAAATACCTTCGTTACGGAAGTTACGGTTGAtt                                                  >  1:1625328/1‑37 (MQ=255)

                                                        aCGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACg               >  1:3649797/1‑71 (MQ=255)

                                                         cagAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAg                  >  1:629623/3‑67 (MQ=255)

                                                         cagAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACgt              >  1:3141714/3‑70 (MQ=255)

                                                         cGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGc              >  1:2166419/1‑71 (MQ=255)

                                                          ggAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCt             >  1:1701368/1‑71 (MQ=255)

                                                          ggAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCt             >  1:2088152/1‑71 (MQ=255)

                                                          agAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACgtt             <  1:3260411/70‑3 (MQ=255)

                                                          agAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACgtt             <  1:1161142/70‑3 (MQ=255)

                                                           gAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCtt            >  1:2154592/1‑71 (MQ=255)

                                                            aaaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGAc                <  1:3478955/66‑1 (MQ=255)

                                                               tACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCgt                                      <  1:3495609/41‑2 (MQ=38)

                                                                  cTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTAc     <  1:2315807/71‑1 (MQ=255)

                                                                   ttCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCaaaac                               >  1:2638097/1‑42 (MQ=25)

                                                                   ttCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa      >  1:3514976/1‑69 (MQ=255)

                                                                     cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGt  >  1:2433687/1‑71 (MQ=255)

TGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGT  >  minE/1933581‑1933720

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