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 2,872,335 C→T 26.9% H196Y (CAT→TAT)  ulaF → L‑ribulose 5‑phosphate 4‑epimerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,872,3350CT26.9% 110.1 / 37.8 96H196Y (CAT→TAT) ulaFL‑ribulose 5‑phosphate 4‑epimerase
Reads supporting (aligned to +/- strand):  ref base C (33/37);  new base T (19/7);  total (52/44)
Fisher's exact test for biased strand distribution p-value = 3.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACGATGCGGTGCATAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGCGTAAACA  >  minE/2872270‑2872397
                                                                 |                                                              
cACGATGCGGTGCATAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCAtt                                                             >  1:2180039/1‑69 (MQ=255)
cACGATGCGGTGCATAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCAtt                                                             >  1:2332336/1‑69 (MQ=255)
cACGATGCGGTGCATAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCAtt                                                             >  1:1406114/1‑69 (MQ=255)
cACGATGCGGTGCATAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCAtt                                                             >  1:75472/1‑69 (MQ=255)
cACGATGCGGTGCATAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCAtt                                                             >  1:2730504/1‑69 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:2669394/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:2082913/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:507081/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:373853/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:2534476/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:2620190/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:2622199/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:684853/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:1253460/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:3082803/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:325488/1‑68 (MQ=255)
              tAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCa                                                >  1:532612/1‑68 (MQ=255)
                aCGCGGTGGTGATGGAAGAAGTGGCTAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAAt                                              <  1:1541384/68‑1 (MQ=255)
                aCGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAAt                                              <  1:632898/68‑1 (MQ=255)
                aCGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAAt                                              <  1:1758937/68‑1 (MQ=255)
                aCGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAAt                                              <  1:586113/68‑1 (MQ=255)
                aCGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAAt                                              <  1:2335985/68‑1 (MQ=255)
                aCGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAAt                                              <  1:1159805/68‑1 (MQ=255)
                     gtggtgATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATc                                        <  1:3210881/69‑1 (MQ=255)
                     gtggtgATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATc                                        <  1:3264715/69‑1 (MQ=255)
                     gtggtgATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATc                                        <  1:385272/69‑1 (MQ=255)
                     gtggtgATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATc                                        <  1:52835/69‑1 (MQ=255)
                     gtggtgATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATc                                        <  1:898143/69‑1 (MQ=255)
                     gtggtgATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATc                                        <  1:1435984/69‑1 (MQ=255)
                     gtggtgATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATc                                        <  1:464791/69‑1 (MQ=255)
                     gtggtgATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATc                                        <  1:1896392/69‑1 (MQ=255)
                        gtgATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGAc                                     >  1:1961525/1‑69 (MQ=255)
                        gtgATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGAc                                     >  1:874158/1‑69 (MQ=255)
                           aTGGAAGAAGTGGCGAAAATGGCGGGGATTGCCCGCGGCATTAACCCACAACTCAAt                                              <  1:67675/57‑1 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCGCGTAGTCTTAACCCACAACTGAATCACATCGACAGCt                                 <  1:760691/68‑1 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCt                                 <  1:1432560/68‑1 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCt                                 <  1:426996/68‑1 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCt                                 <  1:1667743/68‑1 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCt                                 <  1:1527108/68‑1 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCt                                 <  1:1482122/68‑1 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCtt                                >  1:1236352/1‑69 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCtt                                >  1:3194032/1‑69 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCtt                                >  1:2890721/1‑69 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCtt                                >  1:2617375/1‑69 (MQ=255)
                             ggAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCtt                                >  1:319836/1‑69 (MQ=255)
                                agaagTGGCGAAAATGGCGTTGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCt                             <  1:511440/69‑1 (MQ=255)
                                agaagTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCt                             <  1:2115037/69‑1 (MQ=255)
                                    gTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCtgatg                         <  1:2280354/69‑1 (MQ=255)
                                    gTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCtgatg                         <  1:2393675/69‑1 (MQ=255)
                                     tGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCtgatg                         <  1:1786254/68‑1 (MQ=255)
                                          aaaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCt                                 <  1:865353/55‑1 (MQ=255)
                                          aaaaTGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATaaa                   <  1:2818719/69‑1 (MQ=255)
                                          aaaaTGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATaaa                   <  1:335799/69‑1 (MQ=255)
                                          aaaaTGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATaaa                   <  1:343198/69‑1 (MQ=255)
                                          aaaaTGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATaaa                   <  1:860214/69‑1 (MQ=255)
                                          aaaaTGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATaaa                   <  1:383840/69‑1 (MQ=255)
                                          aaaaTGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATaaa                   <  1:1214866/69‑1 (MQ=255)
                                          aaaaTGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATaaa                   <  1:1939814/69‑1 (MQ=255)
                                          aaaaTGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATaaa                   <  1:1985994/69‑1 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCt                                 >  1:1961135/1‑54 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATaaa                   >  1:353862/1‑68 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:457761/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:548105/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:610579/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:1003361/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:1771166/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:1871950/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:800711/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:1906182/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:2029631/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:2083952/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:2168973/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:2355464/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:2452573/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:2532198/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:2614956/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:2834302/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCGCGTAGTATTAACCCACAACTGAATCACATCGACAGCTTCCTGATGAATAAac                  >  1:3114208/1‑69 (MQ=255)
                                           aaaTGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATaaa                   <  1:1559420/68‑1 (MQ=255)
                                               ggCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACtt              <  1:94557/69‑1 (MQ=255)
                                               ggCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACtt              <  1:2174452/69‑1 (MQ=255)
                                               ggCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACtt              <  1:1765879/69‑1 (MQ=255)
                                                gCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTc             >  1:2859824/1‑69 (MQ=255)
                                                     gATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGc         >  1:3074752/1‑68 (MQ=255)
                                                     gATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGc         >  1:2852120/1‑68 (MQ=255)
                                                     gATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGc         >  1:764542/1‑68 (MQ=255)
                                                     gATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGc         >  1:827475/1‑68 (MQ=255)
                                                     gATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGc         >  1:843800/1‑68 (MQ=255)
                                                     gATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGc         >  1:1582685/1‑68 (MQ=255)
                                                     gATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGc         >  1:1456525/1‑68 (MQ=255)
                                                     gATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGc         >  1:1092255/1‑68 (MQ=255)
                                                      aTTGCCCGCGGCATTAACCCACAACTCAATCACATc                                        <  1:1808642/36‑1 (MQ=255)
                                                            cgcgGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGGGTAAaca  <  1:1882870/68‑1 (MQ=255)
                                                            cgcgGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGCGTAAaca  <  1:3036452/68‑1 (MQ=255)
                                                            cgcgGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGCGTAAaca  <  1:2776126/68‑1 (MQ=255)
                                                               ggCATTAACCCACAACTCAATCACATCGACAGCTTCCtgatg                         <  1:3398463/42‑1 (MQ=255)
                                                                 |                                                              
CACGATGCGGTGCATAACGCGGTGGTGATGGAAGAAGTGGCGAAAATGGCGTGGATTGCCCGCGGCATTAACCCACAACTCAATCACATCGACAGCTTCCTGATGAATAAACACTTCATGCGTAAACA  >  minE/2872270‑2872397

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