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 1,904,839 G→A 26.3% G361G (GGC→GGT)  ptr ← protease III

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,904,8390GA26.3% 126.6 / 39.9 106G361G (GGC→GGT) ptrprotease III
Reads supporting (aligned to +/- strand):  ref base G (15/63);  new base A (11/17);  total (26/80)
Fisher's exact test for biased strand distribution p-value = 4.29e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 118 total aligned reads displayed.

TGCCTTTTTCACGTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGTT  >  minE/1904772‑1904907
                                                                   |                                                                    
tGCCTTTTTCACGTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGc                                                                     <  1:1842789/69‑1 (MQ=255)
tGCCTTTTTCACGTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGc                                                                     >  1:2358039/1‑69 (MQ=255)
            gTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTa                                                         <  1:1314402/69‑1 (MQ=255)
            gTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTa                                                         <  1:1566769/69‑1 (MQ=255)
               aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                                      >  1:771261/1‑69 (MQ=255)
               aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                                      >  1:3227794/1‑69 (MQ=255)
               aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                                      >  1:2697065/1‑69 (MQ=255)
               aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                                      >  1:1619456/1‑69 (MQ=255)
               aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                                      >  1:241357/1‑69 (MQ=255)
               aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                                      >  1:3390778/1‑69 (MQ=255)
               aCAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAg                                                      >  1:2758609/1‑69 (MQ=255)
                 aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCTAGGCCTTTATCGGTTAAAGa                                                     <  1:2776393/68‑1 (MQ=255)
                 aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                                     <  1:2167736/68‑1 (MQ=255)
                 aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                                     <  1:2867743/68‑1 (MQ=255)
                 aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                                     <  1:1652508/68‑1 (MQ=255)
                 aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                                     <  1:1333435/68‑1 (MQ=255)
                 aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                                     <  1:2672371/68‑1 (MQ=255)
                 aGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGa                                                     <  1:2465618/68‑1 (MQ=255)
                  gATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACg                                                   <  1:41293/69‑1 (MQ=255)
                  gATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACg                                                   <  1:2612005/69‑1 (MQ=255)
                   aTTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACg                                                   <  1:2969126/68‑1 (MQ=255)
                        gaTAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCagag                                              <  1:142039/68‑1 (MQ=255)
                        gaTAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCagag                                              <  1:2115332/68‑1 (MQ=255)
                        gaTAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCagag                                              <  1:1888246/68‑1 (MQ=255)
                         aTAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGAt                                            >  1:1593642/1‑69 (MQ=255)
                            gCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCg                                          >  1:567758/1‑68 (MQ=255)
                            gCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCg                                          >  1:571185/1‑68 (MQ=255)
                              tAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                                        <  1:1755466/68‑1 (MQ=255)
                               aaaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                                      <  1:1887099/69‑1 (MQ=255)
                               aaaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                                      <  1:1998706/69‑1 (MQ=255)
                               aaaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                                      <  1:3325558/69‑1 (MQ=255)
                                aaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                                      <  1:1803995/68‑1 (MQ=255)
                                aaaaTTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTaa                                      <  1:1045246/68‑1 (MQ=255)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCagag                                              >  1:1336246/2‑55 (MQ=39)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                                >  1:3059383/2‑69 (MQ=255)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                                >  1:1051241/2‑69 (MQ=255)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                                >  1:552858/2‑69 (MQ=255)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                                >  1:2223398/2‑69 (MQ=255)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                                >  1:1447030/2‑69 (MQ=255)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                                >  1:2149646/2‑69 (MQ=255)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                                >  1:1622942/2‑69 (MQ=255)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                                >  1:167008/2‑69 (MQ=255)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                                >  1:1963715/2‑69 (MQ=255)
                                     ggccgccACAACCTGATCGCGATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATAcgcc                                >  1:3090342/2‑69 (MQ=255)
                                               aCCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGTTCGCt                                        <  1:2072117/51‑1 (MQ=255)
                                                  tGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACg                                                   <  1:2153030/37‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:3409191/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:2737630/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:3419663/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:1014081/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:2646501/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:2634024/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:995352/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:1149529/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:1451167/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:1624599/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:170093/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:2155131/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:1087822/68‑1 (MQ=255)
                                                      cgcgATTCGCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:2518432/68‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAATACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc                 <  1:689037/67‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                                        <  1:3033012/44‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                                        <  1:3252798/44‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                                        <  1:2587835/44‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCt                                        <  1:947459/44‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc                 <  1:1103379/67‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc                 <  1:1777374/67‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc                 <  1:1337656/67‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc                 <  1:400096/67‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc                 <  1:1092676/67‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc                 <  1:3361997/67‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGAc                 <  1:1389648/67‑1 (MQ=255)
                                                      cgcgATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAAATCGCt                                        <  1:415756/44‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCTCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:2831465/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:2577223/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:1211298/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:976946/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:614186/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:356581/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:805757/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:1487100/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:3169733/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:2488215/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:2949229/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:2468352/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:2711174/69‑1 (MQ=255)
                                                          aTTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:2449124/69‑1 (MQ=255)
                                                           ttcgCCAGACCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACg                <  1:973215/60‑1 (MQ=255)
                                                           ttAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:468009/68‑1 (MQ=255)
                                                           ttAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAgg           <  1:2059877/68‑1 (MQ=255)
                                                                   gCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGtt  >  1:2573561/1‑69 (MQ=255)
                                                                   gCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGtt  >  1:97427/1‑69 (MQ=255)
                                                                   gCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGtt  >  1:800468/1‑69 (MQ=255)
                                                                   gCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGtt  >  1:2445381/1‑69 (MQ=255)
                                                                   gCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGtt  >  1:2239837/1‑69 (MQ=255)
                                                                   gCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGtt  >  1:2099231/1‑69 (MQ=255)
                                                                   gCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGtt  >  1:192815/1‑69 (MQ=255)
                                                                   gCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGtt  >  1:3092300/1‑69 (MQ=255)
                                                                   gCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGt   >  1:1532725/1‑68 (MQ=255)
                                                                   gCCGTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGtt  >  1:803460/1‑69 (MQ=255)
                                                                   |                                                                    
TGCCTTTTTCACGTAACAGATTGAGATAGCTAAAAATTGCCGCCACAACCTGATCGCGATTAGCCAGGCCTTTATCGGTTAAAGACGCAGAGATCGCTAATACGCCGCTGTTGCCGTTGACGATAGGATCGGAGTT  >  minE/1904772‑1904907

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