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 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 4,066,786 C→T intergenic (+144/‑129) asd → / → glgB aspartate‑semialdehyde dehydrogenase, NAD(P)‑binding/1,4‑alpha‑glucan branching enzyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,066,7860CT85.9% 378.0 / 47.4 142intergenic (+144/‑129)asd/glgBaspartate‑semialdehyde dehydrogenase, NAD(P)‑binding/1,4‑alpha‑glucan branching enzyme
Reads supporting (aligned to +/- strand):  ref base C (13/7);  new base T (61/61);  total (74/68)
Fisher's exact test for biased strand distribution p-value = 2.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 142 total aligned reads displayed.

GATTTACCGGGAGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAGGTCAAAAAAA  >  W3110S.gb/4066718‑4066851
                                                                    |                                                                 
gATTTACCGGGAGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCt                                                                 >  1:682416/1‑71 (MQ=255)
gATTTACCGGGAGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCt                                                                 >  1:1202609/1‑71 (MQ=255)
gATTTACCGGGAGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCt                                                                 >  1:2973426/1‑71 (MQ=255)
gATTTACCGGGAGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCt                                                                 >  1:3113677/1‑71 (MQ=255)
gATTTACCGGGAGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCt                                                                 >  1:332080/1‑71 (MQ=255)
gATTTACCGGCAGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATTAGTATTCACAGTCt                                                                 >  1:3214382/1‑71 (MQ=255)
 aTTTACCGGGAGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCt                                                                 <  1:2647698/70‑1 (MQ=255)
           aGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTg                                                      <  1:2880241/71‑1 (MQ=255)
           aGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTg                                                      <  1:3878978/71‑1 (MQ=255)
           aGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTg                                                      <  1:1637820/71‑1 (MQ=255)
               aaaTAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGga                                                  >  1:2373709/1‑71 (MQ=255)
                    gagCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGGGGacgacg                                             <  1:3007634/71‑1 (MQ=255)
                    gagCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGacgacg                                             <  1:2237919/71‑1 (MQ=255)
                    gagCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGacgacg                                             <  1:4069754/71‑1 (MQ=255)
                    gagCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGacgacg                                             <  1:2380979/71‑1 (MQ=255)
                    gagCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGacgacg                                             <  1:1724498/71‑1 (MQ=255)
                    gagCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGacgacg                                             <  1:2575386/71‑1 (MQ=255)
                    gagCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGacgacg                                             <  1:2580155/71‑1 (MQ=255)
                         ttGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCagag                                        <  1:2169310/71‑1 (MQ=255)
                         ttGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCagag                                        <  1:206893/71‑1 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:3577727/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:204586/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:3764990/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:3683394/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:3394469/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:454489/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:271778/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:654317/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:956102/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:1394075/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:1436833/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:1808449/1‑71 (MQ=255)
                           ggCTATTCTTTAAGGGTGGCTGAATACATGAGTATTAACAGCCTTACCTGAAGTGAGGACGACGCagagag                                      >  1:3282357/1‑71 (MQ=255)
                            gCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCagagag                                      <  1:2420707/70‑1 (MQ=255)
                                   tttAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCagagag                                      <  1:3214522/63‑1 (MQ=255)
                                   tttAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCagagag                                      <  1:2019130/63‑1 (MQ=255)
                                   tttAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCagagag                                      <  1:31483/63‑1 (MQ=255)
                                   tttAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCagagag                                      <  1:2894044/63‑1 (MQ=255)
                                     tAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGa                                    >  1:2088139/1‑63 (MQ=255)
                                     tAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              >  1:332557/1‑69 (MQ=255)
                                     tAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              >  1:3725581/1‑69 (MQ=255)
                                     tAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              >  1:1700366/1‑69 (MQ=255)
                                     tAAGGGTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              >  1:2446337/1‑69 (MQ=255)
                                     tAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              <  1:1025172/69‑1 (MQ=255)
                                     tAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              <  1:2545701/69‑1 (MQ=255)
                                     tAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              <  1:2455393/69‑1 (MQ=255)
                                        gggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAgg                                     <  1:3829155/59‑1 (MQ=255)
                                        gggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACag                             <  1:512286/67‑1 (MQ=255)
                                        gggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACag                             <  1:3478776/67‑1 (MQ=255)
                                        gggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACag                             <  1:1469248/67‑1 (MQ=255)
                                        gggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACag                             <  1:1482645/67‑1 (MQ=255)
                                        gggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACag                             <  1:149731/67‑1 (MQ=255)
                                        gggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACag                             <  1:1900139/67‑1 (MQ=255)
                                         ggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGCCGCAGAGAGGATGCACAGAGtgc                        >  1:2226733/1‑71 (MQ=255)
                                         ggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGtgc                        >  1:3534013/1‑71 (MQ=255)
                                         ggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGtgc                        >  1:777308/1‑71 (MQ=255)
                                         ggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGtgc                        >  1:2032348/1‑71 (MQ=255)
                                         ggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGtgc                        >  1:3309367/1‑71 (MQ=255)
                                         ggTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGtgc                        >  1:3021217/1‑71 (MQ=255)
                                          gTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGga                                                  >  1:1169223/1‑44 (MQ=255)
                                          gTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCaga                                         >  1:1694092/1‑53 (MQ=255)
                                          gTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCaga                                         >  1:466128/1‑53 (MQ=255)
                                          gTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCaga                                         >  1:4033156/1‑53 (MQ=255)
                                          gTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCaga                                         >  1:3383619/1‑53 (MQ=255)
                                          gTGGCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCag                                          >  1:3861252/1‑52 (MQ=255)
                                          gTGGCTGAATAAATGAGTATTCACAGTCTTACATGAAGTGAGGACGACGCaga                                         >  1:1142029/1‑53 (MQ=255)
                                             gCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGtgctgc                     >  1:1211912/1‑70 (MQ=255)
                                             gCTGAATACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTgcg                    >  1:3984468/1‑71 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              <  1:1772909/57‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              <  1:351938/57‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              <  1:2314936/57‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              <  1:426496/57‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCg                 <  1:404453/70‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCg                 <  1:3905788/70‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCg                 <  1:115879/70‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCg                 <  1:2327713/70‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCg                 <  1:2818241/70‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCg                 <  1:2561930/70‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCg                 <  1:3463547/70‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCg                 <  1:3411710/70‑1 (MQ=255)
                                                 aaTACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCg                 <  1:899526/70‑1 (MQ=255)
                                                   tACATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACaga                            >  1:485258/1‑57 (MQ=255)
                                                     cATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAg            <  1:3624506/71‑1 (MQ=255)
                                                     cATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAg            <  1:3144831/71‑1 (MQ=255)
                                                     cATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAg            <  1:2277950/71‑1 (MQ=255)
                                                     cATGAGTATTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAg            <  1:66546/71‑1 (MQ=255)
                                                     cATGAGTATTCACAGCCTTACCTGAAGTGTGGACGACGCAGAGAGGATGcaca                              <  1:835838/53‑1 (MQ=255)
                                                            aTTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGAt                                   >  1:1198493/1‑41 (MQ=255)
                                                            aTTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGcaca                              >  1:3249988/1‑46 (MQ=255)
                                                            aTTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAGGTCaaa      >  1:3961638/1‑70 (MQ=255)
                                                            aTTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAGGTCaaa      >  1:558202/1‑70 (MQ=255)
                                                            aTTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAGGTCaaa      >  1:3052868/1‑70 (MQ=255)
                                                            aTTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAGGTCaaa      >  1:215828/1‑70 (MQ=255)
                                                            aTTCACAGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAGGTCaaa      >  1:1037592/1‑70 (MQ=255)
                                                               cacaGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAGGTCaaaaaaa  >  1:1646334/1‑71 (MQ=255)
                                                               cacaGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAGGTCaaaaaaa  >  1:3074222/1‑71 (MQ=255)
                                                                acaGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGt                          <  1:1517923/46‑1 (MQ=255)
                                                                acaGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGt                          <  1:815666/46‑1 (MQ=255)
                                                                acaGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGt                          <  1:1498759/46‑1 (MQ=255)
                                                                acaGTCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGt                          <  1:1861719/46‑1 (MQ=255)
                                                                    |                                                                 
GATTTACCGGGAGTTAAATAGAGCATTGGCTATTCTTTAAGGGTGGCTGAATACATGAGTATTCACAGCCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCACAGAGTGCTGCGCCGTTCAGGTCAAAAAAA  >  W3110S.gb/4066718‑4066851

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A