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 1,904,833 A→C 25.2% A363A (GCT→GCG)  ptr ← protease III

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,904,8330AC25.2% 144.5 / 58.3 107A363A (GCT→GCG) ptrprotease III
Reads supporting (aligned to +/- strand):  ref base A (17/63);  new base C (11/16);  total (28/79)
Fisher's exact test for biased strand distribution p-value = 7.42e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 107 total aligned reads displayed.

AATGCCTTTTTCACGTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGG  >  minE/1904770‑1904898
                                                               |                                                                 
aaTGCCTTTTTCACGTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAg                                                              >  1:747193/1‑69 (MQ=255)
  tGCCTTTTTCACGTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGc                                                            >  1:2358039/1‑69 (MQ=255)
  tGCCTTTTTCACGTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGc                                                            <  1:1842789/69‑1 (MQ=255)
              gTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTa                                                <  1:1566769/69‑1 (MQ=255)
              gTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTa                                                <  1:1314402/69‑1 (MQ=255)
                 aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                             >  1:771261/1‑69 (MQ=255)
                 aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                             >  1:3390778/1‑69 (MQ=255)
                 aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                             >  1:241357/1‑69 (MQ=255)
                 aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                             >  1:3227794/1‑69 (MQ=255)
                 aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                             >  1:2697065/1‑69 (MQ=255)
                 aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                             >  1:164488/1‑69 (MQ=255)
                 aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                             >  1:2758609/1‑69 (MQ=255)
                 aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                             >  1:1619456/1‑69 (MQ=255)
                   aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCTAGGCCTTTATCGGTTAAAGa                                            <  1:2776393/68‑1 (MQ=255)
                   aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                            <  1:2465618/68‑1 (MQ=255)
                   aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                            <  1:1652508/68‑1 (MQ=255)
                   aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                            <  1:2867743/68‑1 (MQ=255)
                   aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                            <  1:2672371/68‑1 (MQ=255)
                   aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                            <  1:1333435/68‑1 (MQ=255)
                   aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                            <  1:2599130/68‑1 (MQ=255)
                    gATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACg                                          <  1:41293/69‑1 (MQ=255)
                    gATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACg                                          <  1:2612005/69‑1 (MQ=255)
                     aTTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACg                                          <  1:2969126/68‑1 (MQ=255)
                       tGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAg                                                              >  1:2921240/1‑46 (MQ=255)
                          gaTAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCagag                                     <  1:142039/68‑1 (MQ=255)
                          gaTAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCagag                                     <  1:2115332/68‑1 (MQ=255)
                          gaTAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCagag                                     <  1:1888246/68‑1 (MQ=255)
                          gaTAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCagag                                     <  1:1495226/68‑1 (MQ=255)
                           aTAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGAt                                   >  1:2928685/1‑69 (MQ=255)
                           aTAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGAt                                   >  1:1593642/1‑69 (MQ=255)
                              gCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCg                                 >  1:807185/1‑68 (MQ=255)
                              gCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCg                                 >  1:571185/1‑68 (MQ=255)
                              gCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCg                                 >  1:567758/1‑68 (MQ=255)
                                tAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                               <  1:1755466/68‑1 (MQ=255)
                                tAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                               <  1:1134357/68‑1 (MQ=255)
                                 aaaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                             <  1:3325558/69‑1 (MQ=255)
                                 aaaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                             <  1:1887099/69‑1 (MQ=255)
                                 aaaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                             <  1:198816/69‑1 (MQ=255)
                                 aaaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                             <  1:1998706/69‑1 (MQ=255)
                                  aaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                             <  1:1803995/68‑1 (MQ=255)
                                  aaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                             <  1:1045246/68‑1 (MQ=255)
                                       ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCagag                                     >  1:1336246/2‑55 (MQ=39)
                                       ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                       >  1:2149646/2‑69 (MQ=255)
                                       ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                       >  1:3059383/2‑69 (MQ=255)
                                       ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                       >  1:2223398/2‑69 (MQ=255)
                                       ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                       >  1:1963715/2‑69 (MQ=255)
                                       ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                       >  1:1051241/2‑69 (MQ=255)
                                       ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                       >  1:167008/2‑69 (MQ=255)
                                       ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                       >  1:1622942/2‑69 (MQ=255)
                                       ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                       >  1:552858/2‑69 (MQ=255)
                                                 aCCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGTTCGCt                               <  1:2072117/51‑1 (MQ=255)
                                                    tGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACg                                          <  1:2153030/37‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:3419663/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:2737630/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:3409191/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:1014081/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:995352/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:3133219/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:170093/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:1087822/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:1149529/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:1451167/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:1624599/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:2634024/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:2155131/68‑1 (MQ=255)
                                                        cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg       <  1:2518432/68‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAATACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc        <  1:689037/67‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                               <  1:2465734/44‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                               <  1:2587835/44‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                               <  1:947459/44‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                               <  1:3252798/44‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                               <  1:3033012/44‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc        <  1:1092676/67‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc        <  1:1389648/67‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc        <  1:1337656/67‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc        <  1:400096/67‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc        <  1:2275142/67‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc        <  1:3361997/67‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc        <  1:1777374/67‑1 (MQ=255)
                                                        cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc        <  1:1103379/67‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCTCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:2831465/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:2711174/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:2949229/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:614186/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:608393/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:1211298/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:805757/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:2577223/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:2449124/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:356581/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:1487100/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:2488215/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:3383794/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:976946/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:3169733/69‑1 (MQ=255)
                                                            aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:2468352/69‑1 (MQ=255)
                                                             ttAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:413689/68‑1 (MQ=255)
                                                             ttAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:468009/68‑1 (MQ=255)
                                                             ttAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:2059877/68‑1 (MQ=255)
                                                              tAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg  <  1:2116225/67‑1 (MQ=255)
                                                               |                                                                 
AATGCCTTTTTCACGTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGG  >  minE/1904770‑1904898

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