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
A1 F3 I0 R1	560	56.4	4650532	94.9%	4413354	59.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,860,149	G→T	10.2%	A22S (GCA→TCA)	ygbJ →	predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,860,149	0	G	T	10.2%	247.1 / 8.8	78	A22S (GCA→TCA)	ygbJ	predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain
Reads supporting (aligned to +/- strand): ref base G (28/42); new base T (6/2); total (34/44)
Fisher's exact test for biased strand distribution p-value = 7.27e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.89e-01

AGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGAACAGCAATGCCTGCGCTAC  >  W3110S.gb/2860079‑2860216

agagCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGagcag                                                                     <  1:3322660/71‑1 (MQ=255)

 gagCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGagcagc                                                                    <  1:438439/71‑1 (MQ=255)

   gCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCAc                                                                  >  1:382430/1‑71 (MQ=255)

      gATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCATCACTGt                                                               <  1:599364/71‑1 (MQ=255)

        tGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTCAGGGTCAATGGGAATGGGAGCAGCACTGTc                                                              <  1:3024830/70‑1 (MQ=255)

        tGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTCAGGGTCAATGGGAATGGGAGCAGCACTGTc                                                              <  1:3019458/70‑1 (MQ=255)

         gAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                                                             >  1:2662983/1‑70 (MQ=255)

          aaaaCGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTg                                                                <  1:3941501/66‑1 (MQ=255)

          aaaaCGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTg                                                                <  1:4456012/66‑1 (MQ=255)

          aaaaCGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCata                                                           >  1:2747099/1‑71 (MQ=255)

           aaaCGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCatat                                                          <  1:4024290/71‑1 (MQ=255)

            aaCGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATg                                                         >  1:3366610/1‑71 (MQ=255)

              cGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCATCACTGTCa                                                             >  1:3780102/1‑65 (MQ=255)

              cGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCATCACTGTCa                                                             >  1:1685156/1‑65 (MQ=255)

              cGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCATCACTGTCa                                                             >  1:2449906/1‑65 (MQ=255)

                  aTCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGt                                                               <  1:1231010/59‑1 (MQ=255)

                  aTCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGt                                                               <  1:233641/59‑1 (MQ=255)

                   tCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCcg                                                     >  1:1826064/1‑68 (MQ=255)

                    cTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCcgcg                                                   >  1:3023022/1‑69 (MQ=255)

                    cTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCcgcg                                                   >  1:2629979/1‑69 (MQ=255)

                      gAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAg                                                >  1:3774799/1‑70 (MQ=255)

                       aGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGagcag                                                                     >  1:2332197/1‑48 (MQ=255)

                       aGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATTTGTCCgcgc                                                  <  1:154765/67‑1 (MQ=255)

                       aGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCgcgc                                                  <  1:887119/67‑1 (MQ=255)

                       aGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCgcgc                                                  <  1:1404821/67‑1 (MQ=255)

                       aGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCgcgc                                                  <  1:4640292/67‑1 (MQ=255)

                       aGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCgcgc                                                  <  1:791381/67‑1 (MQ=255)

                       aGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGt                                              <  1:1603304/71‑1 (MQ=255)

                        gTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTc                                             >  1:2777110/1‑71 (MQ=255)

                        gTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTc                                             >  1:4347677/1‑71 (MQ=255)

                         tttCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                                                             <  1:2298762/54‑1 (MQ=255)

                         tttCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCt                                            <  1:4217267/71‑1 (MQ=255)

                         tttCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCt                                            <  1:2592391/71‑1 (MQ=255)

                          ttCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCATCACTGTCa                                                             >  1:2414577/1‑53 (MQ=255)

                           tCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCtt                                           <  1:951275/70‑1 (MQ=255)

                             aTGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCt                                        <  1:4013171/71‑1 (MQ=255)

                             aTGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCt                                        <  1:980267/71‑1 (MQ=255)

                             aTGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTCTCATATGTCCGCGCAGGTCTTTc                                         <  1:541851/70‑1 (MQ=255)

                              tGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCATCAc                                                                  <  1:2211512/44‑1 (MQ=255)

                                tCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                                                             <  1:1030127/47‑1 (MQ=255)

                                 cGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCAc                                                                  >  1:79800/1‑41 (MQ=255)

                                 cGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCAc                                                                  >  1:1377275/1‑41 (MQ=255)

                                  ggTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCt                                            <  1:4535010/62‑1 (MQ=255)

                                  ggTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTg                                   <  1:2919572/71‑1 (MQ=255)

                                    tttCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCt                                            <  1:4095913/58‑1 (MQ=255)

                                      tCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCt                                            <  1:4406768/58‑1 (MQ=255)

                                      tCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCt                                        <  1:1092677/62‑1 (MQ=255)

                                        gTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCttt                                          >  1:1147502/1‑58 (MQ=255)

                                        gTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGgcg                              <  1:738466/70‑1 (MQ=255)

                                        gTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGgcg                              <  1:393176/70‑1 (MQ=255)

                                         ttGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTTCGCGCAGGTCTTTCTACCTGGGGCGCa                            <  1:695710/71‑1 (MQ=255)

                                           ggCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAg                           <  1:3548045/70‑1 (MQ=255)

                                           ggCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGa                          >  1:663217/1‑71 (MQ=255)

                                           ggCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGa                          >  1:3866647/1‑71 (MQ=255)

                                             cTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTAc                                      <  1:665275/57‑1 (MQ=255)

                                                aGGGTCAATGGGAATGGGAGCATCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCa                            >  1:3058154/1‑64 (MQ=255)

                                                aGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCttt                                          >  1:1244446/1‑50 (MQ=255)

                                                 gggTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGa                     <  1:960798/70‑1 (MQ=255)

                                                  ggTCAATGGGAATGGGAGCAGCACTGTCACATGTCcgc                                                    <  1:3901526/38‑1 (MQ=255)

                                                    tCAATGGGAATGGGAGCATCACTGTCATATGTCCGCGCAGGt                                              >  1:3967518/1‑42 (MQ=255)

                                                    tCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCt                                        <  1:4212940/48‑1 (MQ=255)

                                                      aatgggaatgggAGCAGCACTGTCATATGTCCGCGCAgg                                               >  1:3507170/1‑39 (MQ=255)

                                                      aatgggaatgggAGCAGCACTGTCATATGTCCGCGCAGGTCt                                            <  1:2822127/42‑1 (MQ=255)

                                                      aatgggaatgggAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGAACAGc                <  1:1276436/70‑1 (MQ=255)

                                                      aatgggaatgggAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGAACAGc                <  1:3016486/70‑1 (MQ=255)

                                                      aatgggaatgggAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGAACAGc                >  1:4000285/1‑70 (MQ=255)

                                                        tgggaatgggaGCAGCACTGTCATATGTCCGCGCa                                                 <  1:3222838/35‑1 (MQ=255)

                                                        tgggaatgggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGAACAGCaa              <  1:4620310/70‑1 (MQ=255)

                                                         gggaatgggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTggg                                 <  1:4116161/50‑1 (MQ=255)

                                                         gggaatgggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTggg                                 <  1:1817537/50‑1 (MQ=255)

                                                          ggaatgggaGCAGCACTGTCATATGTCCGCGCAGGTCt                                            >  1:984721/1‑38 (MQ=255)

                                                          ggaatgggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCa                            >  1:269268/1‑54 (MQ=255)

                                                          ggaatgggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCa                            >  1:1649850/1‑54 (MQ=255)

                                                          ggaatgggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGAc                         >  1:2625028/1‑57 (MQ=255)

                                                          ggaatgggaGCAGCACTGTCATATGTCCGCGAAGGTCTTTCt                                        >  1:2360034/1‑42 (MQ=255)

                                                             atgggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGAACAGCAATGCCTg        >  1:3490936/1‑71 (MQ=255)

                                                               gggaGCAGCACTGTCATATGTCCGCGCAGGTCttt                                          >  1:815107/1‑35 (MQ=255)

                                                               gggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTAcc                                     <  1:2352252/40‑1 (MQ=255)

                                                                ggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCt                       >  1:1539743/1‑53 (MQ=255)

                                                                ggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGAACAGCAATGCCTgcgc     >  1:4520648/1‑71 (MQ=255)

                                                                ggaGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGAACAGCAATGCCTgcgc     >  1:404276/1‑71 (MQ=255)

                                                                   gcatcaCTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGAACAGCAATGCCTGCGCTAc  <  1:1781755/71‑1 (MQ=255)

                                                                    cagcaCTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGAc                         >  1:40755/1‑47 (MQ=255)

AGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCTTTCTACCTGGGGCGCAGACCTGAACAGCAATGCCTGCGCTAC  >  W3110S.gb/2860079‑2860216

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